I've got a few suggestions, actually. I'm just getting back to the game after a LONG hiatus from 4X games in general (this being the only one I play now).
Gameplay Suggestions:
1. Ship customization -- by this, I mean FULL customization. Hull design (graphically speaking, I mean -- not that it'd have an effect on performance), weapon/equipment loadouts, color schemes, etc. Maybe even coloring of your weapon effects and such (that might be a bit much). In terms of the graphical hull design, I'd recommend that the game switch to full 3D models for everything, and that the ships be modular in nature. IE: you could pick a particular overall style, then within that style, select how you wanted the individual parts to look. It's a little out of left field, but City of Heroes (MMORPG where you play as a superhero, if you haven't heard of it) has an incredible character designer that allows for serious customization, all because it's modular and has a WIDE palette for color choices (and each individual piece can have its own primary and secondary colors, as well as individual paint designs, etc.). So, in addition to the actualy "Choose your weapons/armor" stuff that has been a staple since MOO1, I'd say let players seriously customize the look of their ships.
2. Fleet battles -- I know, this one's a tricky one for players, and some are pro and con on this. I'd like to see it added, personally. I'd give players control options, though. You could micro-manage each ship's maneuvers, weapon usage, shield levels, etc., or you could take a more macro-approach where you group ships into squadrons, issue general orders and/or formation orders, and fight the battle that way. More on this in the mechanics section.
3. For those who want REAL micromanagement, a resource/supply logistical spin to the game. IE: some planets are designed well for farming, others for industry, others as a mix. This could be incorporated into a "colony style", complete with specific governor types.
So, for example, your home planet is a "do it all" kind of planet. You then settle a planet that has great agriculture, but lousy mineral resources. Congrats. Your empire has a breadbasket. This planet then acts to supply the next planet you colonize, a Siberian frozen rock of a planet with no agriculture whatsoever, with food. You have to establish supply lines between your planets and protect them. As your game progresses, you could develop technology to help this (IE: jumpgates/controlled wormholes), etc.
This could have SERIOUS implications on gameplay -- including having different planet types benefit different races in different ways. IE: the Yor Collective is entirely mechanical, so worlds with great agriculture are worthless to them. Instead, they crave worlds with high mineral counts AND that orbit certain energy-rich suns. Torians, on the other hand, might prefer aquatic worlds, etc., etc., etc. Basically individual races would have different basic resource needs.
This would have military implications as well. If you find the Dregin "breadbasket" planet, but lack the transports/ground troops to take it, you could blockade it with a fleet, thereby cutting their food supply. Or, if they have a particular mining center of a planet, blockade that planet to close off food from going in, and mineral resources for the rest of the empire from going out. Incidentally, just because a planet harvested a particular resource in one location wouldn't necessarily mean it'd be the manufacturing location.
Finally, trade/economy-wise, this could have a major impact. Let's say the Torians are at war with the Dregin. Their breadbasket planet has fallen, but you, their loyal ally, have decided to support them with a lend-lease system whereby you provide them with regular shipments of food (assuming you've accumulated the right resources, of course).
4. Espionage -- I haven't played with this much in the game, but in general, the espionage system has seemed somewhat overlooked (along with destabilization). I'd like to see it be more useful and able to be controlled more precisely. IE: for destabilization, give players the ability to engage in sabotage, industrial espionage, theft of military secrets, etc. Let players choose how to allocate resources to this effect, or pick which type of mission they'll run.
Mechanics Suggestions:
1. Make the game customizable. For ALL of the additions/options, let players opt-out. IE: if you add fleet combat, let players do it the old way -- where they group their ships and just let 'em slug it out. Or let them micro/macro-manage the battle. When Civ2 added health bars to units, they let you fight the old way still (IE: units either were destroyed or not -- no health bars). Same goes for ALL of the overall systems. If you implement a resource/world-type system like what I suggested above, let players opt-out of having to deal with the hassle of feeding the empire and managing supply lines. I don't just mean "assign an AI governor" either. I mean let the rules allow you to COMPLETELY opt-out. Even do this for spaceship customization. Let players either opt-out of the customizing game, allow the computer to auto-assign designs, or micro-manage the designs as they see fit. WHATEVER gets changed, let people have the option to play "classic" rules, just with some of the new bells and whistles (IE: techs, races, etc.).
2. Auto-turn options. IE: allow players to let the game run automated until event X happens. Allow players to que up building tasks. Yes, it's very MOO2, but so what? Civ3 used a system like this too, and they're made by totally different companies. I remember when I considered MOO1 Civ in space. It was still fun. If it works, don't be afraid to use it just because it's "too close" to some other game. The key questions should be "is it fun, does it work in this game with all the other stuff we have, and do we have the capacity/time/funds to include this feature?"
3. I realize that the game is NOT a combat oriented game (if folks want that, there's the old Battleground series, and Steel Panthers World at War for turn-based combat). However, to the extent that it is included, it'd be nice to see some options for tactical depth. As it stands, it's really more of a "whose ship is tougher" question. Much like the original Civilization. You may get a lucky roll, or you may lose out and be destroyed. But pretty much it's attack an enemy unit, watch a .25 second animation, and combat is over. Again, I STRONGLY urge that this be an OPTIONAL portion of the game, but I'd like to see more depth all around in terms of combat. The ship-to-ship combat could be done tactically, ship-to-planet/orbital combat could be done tactically, and then ground combat could have a slight tactical phase as well, perhaps consisting of deployment, one or two orders phases, and the end of the round. Ground combat could last until the enemy surrendered (which, with certain races, might yield different results -- IE: Altarians spare them, Dregin eat them, Yor Collective enslaves them, etc.), or was destroyed.
Actually, you could skip the actual combat tactics, and develop ground combat in an entirely new (at least to me) way. The same level of ship customization that you could permit (as I describe above) could be applied to ground combat and all combat units. Outfit certain units with certain types of armor, weapons, gear, etc. Assing specific roles to troop types. Then, sub-divide military production into Space and Ground military production. You could opt to channel all military production to your space line, or to your ground line, or split and build both. Then use your intel to determine the enemy's strength, what type of world they live on, what kind of fighting there'd be, and deploy accordingly.
So, for example, let's say your enemy is on a pastoral world with wide rolling plains. You'd want a combination of ground units with speed and ground units with good range and sensors, since vision would be largely unobstructed. You could send a transport with tanks, jetpack and hovercycle troops, and general assault troops (and some artillery for good measure). Or, the world you're attacking is an urban world with dense cities. So, you'll want to leave the less maneuverable tanks at home, and bring in your close-combat troops. Ground combat would play out as it does now (largely by the numbers), but you'd have more tactical input on the front end by designing and determining which units to employ in a given planetary assault.
Anyway, sorry for the Russian novel of a post there, but those were just some ideas I came up with. Whaddaya think, sirs (and madams, if you're out there)?