To cut to the chase, one thing that sort of bothered me a bout gal civ 2 is that the tech boiled down to 3 different versions of "damage" with very little variation. Battles were basically a way of turning tech advantage into military victory, while actual strategy in ship design or fleet composition was lacking. You basically had 3 weapons with 3 defenses and the only question was did they opponent have the tech/designs to handle your weapon type. I still loved the game due to its empire building, but was unimpressed with how combat felt like a formality or equation rather than a real portion of the gameplay.
From what I know of gal civ 3 there isn't that much more to the combat(it will not be controllable correct?) which is fine, but will we at least see more variety to weapons and their effects? I've heard carriers are confirmed(which brings some interesting implications), but one thing i loved about MOO 2 that almost no space 4x has replicated was the variety to the weaponry. Granted it wasn't balanced, and it was mostly possible because you had direct control over the battles, but i'd like to see a little more strategy and synergy rather than the previous 'if you have X win, if you don't ,lose".