Well I'd like to see hybrid modules, like for my "trade/influence starbase" a speed boost for all friendly units.
I'd love a stargate type module where it required 2 gates to be usable. I'd say that transport should be 1 turn between gate's not instantly (keeping all movement points on the ships), even though it'd be more realistic that way but balance.
I'd like for Military star bases to not just boost force but be able to use their force against units in their area...thus am intrigued by the docking concept it'd be great to be able to set a patrol squad and a star base defence squad 0 hyperdrive all offence/defence, minimal life support.
I'd love for there to be an Artificial Planet (turning a starbase into a barren world).
I'd love for there to be a space based construction for Medium and bigger vessels. It's hard to conceive building a ship on a planet in the sizes of Large and Huge hulls to fly outside the atmosphere.
I'd be happy to see our worlds autobuild civilian trade/shipping networks vs. us in control of that...depending on the Government type chosen. A dictatorship, or a species that uses mind control, hive mind, computer etc. would be in more control of their society than a Democracy/Republic/Federation. Yes, there would exist rules, but their would be those who break, bend, etc. I noticed there were other options not enabled in Gal Civ 2 like Crime and Cabinet that could be implemented. Granted that's if it's fun!
back to Original Post's question additional starbase modules I'd like to see.
Repair, Star Gate, Artifical Planet, Continuous improvement on weapons/defencive systems based on what tech's I have, Mine Deployer, Moral Booster, Industrial Complexes, Trade lanes, Sensor Enhancements, Electronic Counter Measures (stealth/cloaking/detection/reduction in enemy accuracy). Doom Star Construction. Asteroid base boost [they send resources to the space station, boosting the station which in turn boosts the colon(y/ies) in range] Increased force projection (star base effective range for abilities increased), Logistics increaser (adding starbases to an area increases logistics caps in area).
I agree that upgraded starbases should have huge hitpoints, and be able to take on at least one decent fleet if they're fully upgraded and teched out alone...more so with a docked fleet/defence force... I'd also like to see stations being able to be captured (not just destroyed).