Although Galactic Civilisations 2 is my favourite TBS game, certain things about it really bug me. As with pretty much every TBS, combat is based on virtual dice roles with very little player input at all, and with only three weapon and defence types and hull sizes below medium becoming almost entirely redundant in combat roles by the mid-late game, it can be kinda disappointing.
I would change it so that instead of being a little movie of your ships exchanging particle effects with the enemy, you could have the option of going into a sort of 'commander' mode, where you order your ships to target enemies, move and all the likes kinda like a mini-tabletop game, where ships have a certain number of action points that can be used accordingly, as well energy that would have to be managed.
With this change, I would give each weapon class its own characteristics as well as adding branching weapon trees that added a bit variety to the mix by having different characteristics like precision, projectile velocity, spread, lines of fire, turret mountable, range, damage, etc., etc. Targeting systems could also be added to increase ship accuracy.
Same goes for defences: branching trees with different characteristics, with each type also having its own overarching attributes, like armour protecting whole faces against both mass and missile damage, but not completely. Point defences can negate missile damage entirely and in some cases damage fighters, but have a limited area of influence and must be actively engaged. Shields would work in a similar way, but against beams. Activating them takes energy, with their defence rating correlating with power allocated to shields.
Ship dimensions would also play a role in combat, with smaller exposed faces being harder to hit than big, broad ones, making hull design actually mean something. The smaller hulls would actually have a use later on by coming in squadrons, being harder to hit and using fewer action points to move, making them useful for getting in close to larger ships to deliver their payloads, the downside being fewer hitpoints, significantly shorter ranges (unless unmanned) and being unable to move more than one square per turn in the galaxy view. To compensate, I would add hangar modules to facilitate fighter movement with a fleet.
There are a few other things I would add and change, but it's late and I'm tired, so I'll leave it at that.