Well, works for me. I'm dropping the ability to escort ships in the area of effect, because it was doing per ship, and I wanted per fleet. And it did seem like just too many fighters.  So planets, yards, and bases get these guardian fighters. 

Arguably the fighters have rudimentary hyperdrives that require frequent refueling, and there is a refuel network in the area of effect coordinated by the MSB. 

Simplest explanation (if one is even needed...) would be that there's a non-combat short-range carrier stationed in the starbase that can hyper-hop the radius distance. It's not shown on the map because it's abstracted away as it doesn't take part in the action. It just brings in the fighters, hops away to safety, and comes back later for a pickup if the battle was won. All nice and tidy.

I would also accept the concept of a new (old) kind of hyperdrive system that cannot actually enter hyperdrive essentially creating a one way corridor to the target destination. Once combat has ended they could be picked up by a civilian carrier. 

Military SB's by themselves won't cut it and I also don't use them.  But if I could add all the military stuff to other SB's (like mining) then I'll use it.  Right now it's cheaper to place a mining SB and if it's destroyed just rebuild it with 1-X constructors.  I use fleets as the protection.

Was that testing only one starbase? Would stacking multiple bases boost the effect?

I used them all the time in GC2. They had bonuses to ships combat within their ZOC that were useful.  The MSB in GAC3 are currently not worth building.

There are 25 modules specifically for military starbases, and another 43 generic modules (and you won't always be able to or need to build all of the generic modules, but I'll count them all anyways). Therefore, at worst, I need 68 construction modules to fully build a military starbase. Each construction module costs 27 manufacturing; that's 1836 manufacturing points. By the time I can fully upgrade a military starbase, I ought to be able to build huge-hulled ships with max tech components; let's compute the cost of an example design:

5 Nightmare Torpedoes costing 22 capacity and 128 manufacturing each, 2 Zero Point Armor plates costing 16 capacity and 161 manufacturing each, 2 Invulnerability Field generators costing 10 capacity and 259 manufacturing each, 2 Arreon Missile Defense systems at 13 capacity and 198 manufacturing each, and 3 Stellar Folders at 20 capacity and 136 mass each, for a total cost of 2284 manufacturing and 248 required capacity for components; toss in the hull and that's 2716 manufacturing.

The minimum cost of a fully-upgraded military starbase is roughly two thirds that of a Huge-hulled ship equipped with the kinds of components which are available at the point when you can fully upgrade a military starbase when that Huge-hulled ship for some reason has only the base hull capacity to play with. Now, granted, you're not just going to be floating construction modules out to the station; at minimum, you need to pay for the hull (if cargo, then that increases the cost per point to 69, which increases the overall cost for 68 construction modules to 4692, though you can reduce this by stacking multiple cargo modules on the same cargo hull rather than getting a cargo hull per construction module). This is still an overall manufacturing cost comparable to 1.5 similarly-advanced Huge-hulled ships designed to fit within the base capacity of a huge hull (or just 1 if we double up on the construction modules). Even if we put 4 Hyperdrive Pluses and a Construction Module on each cargo hull, we're only looking at a total manufacturing cost of ~7500, equivalent to ~3 similarly-advanced Huge-hulled ships designed to fill the base hull capacity; this is a small and not particularly advanced fleet by this stage of the game. Even if we put 3 Warp Drives (base of 13 actions per turn) and a Construction Module on each Cargo hull, we're only looking at a cost of ~12000 manufacturing for 68 of these ships, or approximately ~4.5 of the similarly-advanced Huge-hulled ships designed for the base hull capacity (there is not, incidentally, any real point in going for Stellar Folders with the cargo hulls given that we want to keep the total capacity required for each of the designs presented similar; switching to Stellar Folding from Warp Drives increases the cost per ship from 180 to 341 and has no effect on the vessel's movement rate while only saving 8 capacity, modified by any drive capacity requirement reductions you have).

Even being very generous to the military starbase (counting the quality-of-life improvements on the construction ships towards the station cost without discount, having only one construction point per construction ship, using a huge-hulled ship which is similarly-advanced but isn't taking advantage of the capacity bonuses your faction should have by this point in the game), a military starbase doesn't cost any more than a handful of similarly advanced ships do. If we're being more reasonable, it probably costs something more in line with the cost of one similarly advanced ship. Given that fully-upgraded military starbases roughly double the power of each friendly ship within their area of effect, I do not see making the military starbases more powerful on their own as either necessary or reasonable. I also do not view it as at all appropriate for any starbase to be capable of engaging a similarly-advanced nearly-full-scale fleet without supporting units while still having a reasonable chance of surviving the encounter unless you also take away the starbase's ability to be supported by fleet units.

The problem that the military starbase has is not that its bonuses are insufficiently powerful (the first ones you add, sure, but not by the point it's fully upgraded) so much as that they're not necessary (why build a starbase to help my fleet out when my fleet already easily wins each engagement?), and to a lesser extent that the way the bonuses are backloaded rather than frontloaded makes it difficult to use military starbases offensively. Plus there's the issue of whether or not I want to bother investing in something that's only going to be useful for a handful of turns in a game lasting several hundred; the way the game's wars work, you're usually only looking at stable frontier over long time periods when you're at peace with your neighbors.

A few things spring to mind.

1) The cost of 1 huge hulled ship is, presently, 1 turn. Forget the manu cost, as it's irrelevant; any half-decent player can make every planet pump out 3k+ a turn and so produce any ship in 1 go. The cost of the fully-upgraded military starbase is, if we use huge-hull constructors with 5 construction modules, 5 turns. 

2). Those huge-hull ships have 500 hit points each which can be increased with tech and equipment. The MSB is capped at 200. 

3) MSB range, even with the extender modules, is currently miniscule compared to even mid-game ship movement rates, making them useless for anything aside from buffing planet defense fleets.

Now, I'm inclined to agree with Joe that actually, the combat bonuses from MSBs are more than sufficient. You get over 100% increase to every combat stat on ship in it's range. This is an enormous bonus. If the average ship is 50% weapons/armour, then this is equivalent to a 50% mass increase, which effectively multiplies with other mass increases. MSBs do not need more bonuses within their area of effect.

However, the short area of effect of SBs in relation to the movement of late-game ships makes them useless; the ease with which player-designed fleets mince AI-designed fleets makes the bonus unnecessary; and their comparatively pitiful staying power to their high time-construction cost all make them an exceedingly poor investment right now.

This is not a problem with MSBs. It is a problem emerging from other balance issues. Those balance issues are:

1) Rampant over-production that makes ship manu costs a joke

2) Rampantly over-powered engines that makes their area of effect a joke

3) Poor AI ship design and fleet composition that ensures the player can pretty much always win battles (especially the AI fleets being limited to 1 attack per turn) which means additional bonuses are not required.

Just about the only area where military star bases are under-powered in my eyes is their static hit points. A small increase in HP per module to allow a high-end MSB to stand toe-to-toe with one or two huge hulls, to prevent expensive investments being taken out by lone wolf Large hulls, combined with needed fixes in the above three areas, would make them much more attractive.

Then station a fleet at the starbase. I cannot kill the starbase without going through at least that one fleet, and that one fleet is ~twice as strong as the ships in it are supposed to be. "Solving" the vulnerability issue by making the starbases essentially invulnerable (because you require a more advanced fleet to kill the starbase; stack a fleet on a starbase which can already handle a fleet of ships more advanced than the station is and the stations become nearly unkillable) is a bad solution to something that isn't much of an issue and doesn't do anything at all for the issues that the station actually has - namely, that the stations are difficult to use (due to the small area of effect relative and due to the backloaded bonuses), that the stations are currently unnecessary, and that the time in which a military starbase is useful is very limited because the war won't stick around in its area of effect all that long. Making the starbase harder to kill helps these issues how?

I have no objection to making a starbase able to survive lone raiders or other very low force commitments; that, to me, is reasonable. But to demand that the destruction of a starbase requires a more advanced fleet to attack the starbase is simply ridiculous, especially since the player (and the computer) is actually, you know, allowed to allocate fleet assets to defend the starbase by fighting in the same action as the station, and since the fleet assigned to the station is benefiting from the station's bonuses, the attacker probably needs to commit more than just 1 equivalent ship per defending ship stationed at the starbase.

Only 5 construction modules per Huge-hulled construction ship? By the time you can build Huge hulls, you can easily have:

• A Hyperion Shrinker giving roughly +50% hull capacity (10% base, +5% per level; built adjacent to an Elerium Defense Shield for 3 levels, an Antimatter Power Plant for another 2 levels, and a Preparedness Center or the two basic planetary defense structures - military academy and planetary defense system - for another two levels, you'll have a total of +45% hull capacity from the Shrinker, and you can more or less guarantee you'll manage to set this up as long as Antimatter and Elerium exist on the map)
• A hull capacity bonus of up to 50% from specializations you have to go through to get to Huge hulls
• You may also have deposits of Helios Ore at +5% hull capacity per deposit or had the Design Revolution event at least once with the option of taking +10% hull capacity per event

You can fairly easily be looking at a Huge hull with 500+ capacity when it first becomes available; even if the only hull capacity bonus you have is from the Hyperion Shrinker, you're still looking at something like 375 capacity (362.5 if the Hyperion Shrinker has only 7 levels like the one in the bullet, 375 or more if you can get at least one more level onto the Shrinker). If you're going to be using Huge-hulled construction ships, you may as well start by putting 7 construction modules on the hull; that's only 315 capacity (without Transport Specialization), leaving you with ~50 or more capacity for quality-of-life improvements like Warp Drives (room for 3 even without size reduction, giving a respectable speed of 13 + bonuses to the construction ship) even at the low end of the possible hull capacities.

If you've gone all out for capacity increases, you're more likely looking at a 500-capacity Huge hull (and may be looking at something with more capacity, depending on how good of a spot you found for your Shrinker and how lucky you've been with getting Design Revolutions and Helios Ore), which'll fit 10 full-size construction modules and leave you 50 capacity for QoL components, or 14 reduced-size construction modules (Transport Specialization) with 59 capacity left over for QoL components. That's ~2 turns of construction to get every or almost every module specifically for the military starbase (and frankly, I wouldn't miss the four modules affecting the strategic and tactical speeds of ships too much, and if the Military Starbase modules work like the Economic Starbase modules, I won't miss the Sector Defense Grid that much either since it's only another 10% to each attack and defense score over what the preceding module gave), or only 1 turn of construction if you've gotten the doubled construction points bonus from the Pragmatic tree.

By the time you have huge hulls, the cost of the military starbase's exclusive modules can be as little as 1 shipyard-turn of construction time, and completely building out a 68-module station can be as little as three shipyard-turns of construction time, and the designs as given have sufficient capacity beyond the construction modules to allow the vessels to be reasonably fast (13+ moves per turn, possibly better with drive mass reduction tech or speed bonuses, which is not great for late-game ships but is still reasonable even on the larger map sizes unless you're literally sending the ship halfway across the map or something like that) and have more than the minimum range.

You know this is not how things work.  My fleet with their super engines can move in, kill the SB and move out all in one turn.  There is nothing forcing me to fight that fleet first.  And what you are proposing means you have to have a huge fleet next to every MSB out there.  In that case why even have the MSB with all those fleets around?

Have you never noticed that you can fleet ships up with a starbase, or that the starbase's logistical limit for defending ships is similar to end-game logistical limits for fleets? You station ships at the starbase, and that starbase cannot be engaged without involving those ships, and the way the battle mechanics work, the starbase isn't going to be attacked before those ships are destroyed. A fully-developed military starbase increases the power of an individual ship by such a degree that I probably only need about two thirds as many ships at the starbase as you send against it to be fielding a comparable force, and even in the end game that should be within reach given the logistical limit at the starbase and the attainable fleet logistics limits; if the starbase is also so powerful on its own that only a more advanced fleet actually stands a reasonable chance of killing the station, you've made the starbase effectively unkillable, especially by the end game when there are no more advanced fleets to be had.

You want to protect a starbase of any kind, including military, from similarly-advanced fleets? Put a fleet of your own on the station. Starbase defenses should be (but aren't really) capable of handling minor forces, like lone raiders or a small fleet (i.e. one that isn't close to the logistics limit, given that the starbase and the fleet are fielded by similarly advanced empires; if the small fleet is close to the logistics limit, then the starbase should be more advanced than the fleet in order for the starbase to be capable of taking the fleet on and expect victory, except in the very early stages of the game).

Military starbases are force multipliers, not fleet replacements. I need to have a fleet in the area anyways to protect whatever I'm trying to help defend with the military starbase, and if you're sending large fleets into the region to attempt to take it then the fleet(s) I have in the area need to be at least comparable in strength (so midsize fleets with starbase support or large fleets without) if it's reasonable for me to expect to contest your invasion; one of those fleets may as well be stationed at the starbase. As far as the fleet being out of position when you attack the starbase? That's not an issue; that's good baiting on your part, me being careless or overconfident, or me committing an inadequate amount of force to the region for the level of force that you've committed. It is entirely reasonable for you to be able to kill a military starbase with a big fleet if I've made an error in my defensive deployments; if my defensive strategy relies on an asset like a military starbase, I should have to make certain that I provide that asset with an adequate level of protection for the threats to which it may be exposed, or there is no real cost to me making a mistake. "Oh dear, I sent the Fifth Station Defense Fleet too far away to return to its post at the end of this turn. Too bad military starbases are only effectively killable by more advanced fleets, or this mistake might have actually, I don't know, cost me something if my opponent tried to take advantage of it, rather than costing me nothing since the fleet isn't actually needed to defend the station."

1. You only need a fleet at each starbase which is actively threatened or which you expect to be threatened in the near future, not every starbase. Beyond that, you have the option of deciding that a region is not important enough to commit (significant) forces into to protect the assets in the area if you feel that you don't have the available forces necessary to do both that and whatever else you wanted to do. Priorities are a thing, and if defending Nowheresburg V and the associated starbase(s) isn't high enough on the list for me to commit enough forces there to repel whatever you're sending, well, that's too bad for Nowheresburg V and the associated starbase(s). My assets should not be immune to attack even when I fail to provide adequate protection, but with what you're asking, the starbases at the least more or less would be.
2. You can move the fleet out, you just need it to come back before your turn ends or you expose the starbase. Same deal with any garrison - keeping it on station keeps its home safe, but prevents you from making full use of the force thus committed. This is true even if you use interception fleets rather than starbases with garrison fleets; you need a certain minimum density of interception fleets, and you need them to be in the right places, or your fleets won't do anything for you. Beyond that, military starbases have a base game option to help deal with stationed fleets needing to be able to go out, intercept a target, and return - the Stellar Wake Generator, which halves the cost of moving through tiles in the area of effect. The failing is that the area of effect isn't large enough to matter a great deal, especially in the late game.

Besides which, if you're going to have a military starbase in the area, you at present must have at least one fleet nearby anyways if you're to see any real benefit from the military starbase.

One more option can be a drive-disruption effect that slows enemy movement. I think 2-3 tiles' distance should make it balanced. Especially brutal, if you stack a lot of assist-type bonuses, letting your fleet tear the enemies up while they're mired down. You can say that having a secret frequency to tune your own ships' crud will immunize them while having this effect on hostiles.