Fleet mechanics.
Clicking on a fleet with a unit should always join it. Producing with the fleet as a way point should join all ships. No exceptions. The auto-join features are just fine for making exceptions for things you don't think are supposed to be in a fleet, but if I want to add a siege frigate, I should be able to, stupid or not, without having to redo the fleet. They're hard to keep track of when you keep remaking them. It's much wasted effort.
The much mentioned capital ship fleet leader bombing the planet while the well is occupied still could use changing. They engage hostiles still, but ignoring the civ structures when you have a bombing fleet already there to do the job faster is a wee bit of micromanagement. If capital ships weren't the perfect and only good choice for a fleet leader it wouldn't be a problem, but as is it's a lethal one.
AI.
I like that they run away instead of getting butchered, it's smart. They don't seem to grasp the concept of collateral damage though. It's ok to stay and fight with 100 cobalts(a fleet that shouldn't exist in the first place, it sucks) and lose them all in return for a good chunk of the slightly larger army. It's idiotic to run away when it's to give away a planet. Running away with high level capital ships when they're going to get whipped makes perfect sense when it's not for a worthy cause, but the fodder should stand and die. Even high level capital ships shouldn't be retreating away from an improved planet with a large static defense present, they should be retreating to the defenses and slugging it out as long as possible.
Research... Differing AI types is nice, but I swear, research is the only one that is almost challenging. 200 cobalts just isn't a threat. 2000 cobalts isn't much more of one unless you're Vasari. The other AI types need to research things. Research heavy AI should be going to town on the upgrades, but they never even approach the level of research that I do, and I'm an expansionist, not a research whore. I frequently have nothing running and am horribly late to upgrade things in favor of setting up defenses and a large fleet to field on my multi-front wars. Priorities need to be prioritized instead of becoming purist.
Improvements. I swear, the AI is obsessed with infrastructure, but just doesn't build defensive shit. I go into many a well where there's one bloody turret, the defensive AI seem to like pairs of repair platforms with a turret next to each. One turret is just wasted resources, that's not a delaying force. That wont even kill a siege frigate before it gets past it to the other side of the planet. I want to pop my scout into a fortress world bristling with missile turrets surrounding a few repair platforms and hangers with a jammer thrown in for good measure.
Unit AI.
I shit you not, I have never seen the Vasari armor and hull buff auto-cast. That rat bastard overseer just sits there jacking off. The turd should be popping one off on any unit who's shields have or are about to drop. The Dunov shield restore not wasting itself on frigates all the time is nice, if I have a choice, leave it, but it doesn't auto-cast even when it's the only capital ship, very sad.
Pursuit, past the target... Very common. A cobalt closes to range, and closes some more, the target flees, the cobalt chases, the target stops, the cobalt stops after getting out of the firing fiend and coming to rest adjacent to it? Intelligent stopping would be when in range, or at some point inside that for a buffer zone on further flight, not to the point where it has to turn to re-target and robs itself of the rear advantage.
Logistics.
I hates it, I really hates it. The 2k cap isn't really low on a random huge, it's just inadequate for defending three star systems against all 9 remaining ai with 2k fleet points in cobalts. I just can't stress how irritating it is to be trying to kill a few thousand cobalts. You can still win with the right tactics, but it has progressed from fun to annoying by that point. It's actually become that some time around the point where you conquer the first star, but it's at least manageable.
I like the 2k cap not, but I like the research based fleet points even less. The upkeep system as a trade-off for a larger fleet is great, the fleet independent of territory is not. A pseudo return to the old ways, logistics from planets, but with a modifier from the fleet research with the accompanying upkeep is what I'm leaning towards as a fix. The cap can go bye bye too, the game doesn't need one. With allegiance modifiers you're never in danger of having absurd fleet counts. It will always be marginal gains as you spread further out. Any limitations of the hardware will come from the sheer size of the universe being played on. 2k fleet limit on a random small is preposterous, 2k fleet limit on a random huge is a little inadequate, but mainly it just utterly blows that you've got 2k with two full stars under your belt, and even the poor bastard with two planets left is still running around with 400 cobalts and a couple capital ship.
There's nothing wrong with losing when you're losing, and winning when you're winning. It's silly to have a system that keeps you damn near even when you've got a 4-1 advantage in strength.
Defenses.
PJI's blow, established I think. I dislike the stops all traffic version, it's a little much, but considering how easy they are to blow up, stopping all traffic past them wasn't that big a deal. A lot of "how will you blow up the super weapon" talk, but how will you stop someone from blowing it up with them? All I have to do is bring a couple high level sova's loaded with bombers, and send them right at it, poof, no more pji. With an anti-matter store to do so, a gravity warhead type pulse that would autocast as soon as enemy ships tried to jump out would be just fine. If it builds with zero antimatter, you can't trap someone there without them having been able to scout it first and avoid the problem. It also wouldn't need to be that big of a delay, thirty seconds is not a death trap unless it was a death trap when you went in. It would be more than enough to destroy the ping-pong army of death(by irritation) and allow your defending fleets to chase down and destroy penetrating fleets that were going after your softer interior. Consider making it a much more beefy structure as well, much tougher than turrets, but with a fairly high cost in tac points, like 10. This is especially true if they end up returning to a beta style implementation. Then you wont have people spamming them, and they wont be a single pass bomber run to blow up while traveling through the well to the other side. They weren't particularly effective at stopping a carrier heavy fleet, unless you built a dozen of them, in which case it took you forever to get out of the system.
Turrets, hangars and repair platforms. I like the repair platform, change nothing there. Hangars seem to blow up a wee bit fast for their investment, they could probably use a little more armor. Turrets, more range I don't like. More damage I could go along with. They're nice and tough, and dish it out, eventually. They're also short enough in range that it takes effort to try and protect everything. Siege frigates kill planets faster than they kill them, but other than that they're just fine. There is one serious deficiency though. Turrets should not be prioritizing capital ships. Sorry, but trying and failing to kill the 2k shields with 65% mitigation and 4k hull points with 12 armor is a really dumb move when there are two dozen cobalts doing vastly more damage than would all die in far less time than that lone Kol will. If you do increase the damage or range, only do one, not both. Powerful, fleet destroying turrets that outrange the missile frigates designed to combat them is not a good thing...
Capital ship commentary.
A bit of talk on capital ships not being "capital" enough. What is enough? With a few levels, they are vastly more powerful than any comparable expenditure. If you're trying to kill heavy cruisers with a single dunov, yeah, you're screwed. But five kodiaks kill a high level dreadnought? Not a chance. Maybe against the upgrade-less wonder of an AI, but there's no way a level 6 Kol is getting dropped by five kodiaks of similar research improvements. You'd be hard pressed to manage it against a level 3. With the proper support, they are near invincible killing machines, capable of withstanding huge fleets and making it out alive. TEC in particular have excellent synergies between their high level capital ships for obscene survival capabilities. If they were much tougher, there wouldn't be any reason to build frigates and cruisers at all. Protect them, buy the low levels when you can, they're bloody ridiculous after they get their level 6 abilities.