I love GalCiv2 and I'm eagerly awaiting the expansion. That said, it does have its problems (Some of which are being corrected).
I dont like the fact that without planetary invasion, you cant damage someone elses planet at all. If you dont care about keeping the planet, or even dont really want to grab it anyways, it's a bit to easy to exploit the ground combat system. Just send in 1 soldier and use the more destructive conquering techniques (Like Tidal Waves, or Core Detonation). I'd like being able to put in orbital/planet based defenses beyond just stationing ships in orbit, too.
The Tech tree is a bit monotonous. I'd like it to be a bit more interweaving. It's more like a cadelabra then a tree.
Everyone can colonise the exact same worlds. There's no real variety beyond special tiles and PQ. (This is being changed in the expansion)
Espionage is boring. (This is also being changed in the expansion)
I'd like a bit more control over the space combat. I dont require controlling each individual move, but I'd like to be able to prioritize certain targets and issue simple commands. (Concentrate all fire on that Super Star Destroyer!) I'd like the weapon types to have a bit more variety beyond getting past defenses, too. Additionally, I think the first strike is way to important and would like ways to randomize that a bit (Which also opens up the idea for components/research that improves your initiative)