I'm still relatively new to playing GalCiv2 but two things stand out as issues that could easily be fixed to greatly improve gameplay (and I intend to mod them for myself):
Range - It's far too easy to build ships that have enough range to travel across the largest galaxy size. Range should be reworked and at maximum it should be maybe 20% of the distance across the galaxy. This would *force* building of starbases in order to reach enemy space. This would add a lot of strategy to playing.
Speed - same as range, it should be very limited. I've read posts of people that managed to build 100+ speed ships. As a guess I'd say about 20 should be maximum speed. I'm very early into a game (one and a half years in and I've got ships travelling 11 - and I suspect I could build a much faster ship if I designed only for speed).
This is going to be a matter of taste. Some players will like fast, major conflict. While others (like myself) desire a slow, long game of exploration.