Three modules it would be nice to see (although all three would likely complicate the AI greatly):
A) I'd love to see the Asteroid Miner module from GC2 come back. I don't like the new system, and I think building mines rather than buying them is a better dynamic (and buying them just means the AI will have tons and you will have none). And it gives raiders another target.
I'd like to see some kind of Starliner, a module that carries population, but cannot itself colonize or invade. It could be used to add a few more people to a transport or colony ship, or just to move population among worlds. It could also be used set up a 'Galactic Cruise Line' which would work like a trade route, except instead of bringing money it brings tourism bonuses to both factions.
C) I'd like to see a tanker module, which would allow all faction ships within a certain radius (say, six hexes) to be considered to be within life support range even if they are outside of ordinary life support range. SO, it has a 'life support bubble' around it. This would allow expeditionary forces to travel long distances without leaving a trail of starbases behind them, at the expense of having a very fragile logistics chain.