Overall I really love this game, but there are a couple things missing that I find very frustrating:
I really wish GalCiv included actual BORDERS, including open/closed border agreements, etc. It's really annoying that one empire can send a huge war fleet into another and they can't be asked to withdraw their ships or anything. The target civ is forced to either declare war first themselves (incurring a diplomatic penalty just for defending themselves) or else let the invaders choose their target planet with impunity - often being forced to split up their defenses among multiple planets all in range of the invading fleet (like a knight's "forking" maneuver in chess).
There really needs to be some way for an empire to control who enters their territory (especially with warships) and allowing the owner of that territory to defend themselves without incurring diplomatic repercussions.
ALSO (and this one is really simple): There really needs to be some way to click on a starbase and see exactly which modules are still available to build there without having to send a constructor there (often to find there is nothing there you want to build and forcing you to waste more time sending that constructor somewhere else).