The ability to preview a modded tech tree before going in-game.  I've lost count of the number of times I have grouped techs together and then found that they're not in a straightforward left-to-right order as you would expect.  Exit game, re-arrange, jump back in, hope that they're in some kind of sensible order.  It's annoying!

Honestly I'd like a reduction in number of starbases, but increase in their power.  Perhaps to a point where they could become small colonies themselves!

Also additional colonization options along with new initial colony options (Where u can upgrade the initial colony to something else in later game).  For example instead of building a tech capital, why not have the option of upgrading the colony building into a tech capital? 

Finally do something with engines... Seem not so useful in most cases.  And add other core systems maybe, like targeting systems, and advanced defense systems that have strange stats like +1 shields +2 anti missile module.  Lastly more misc modules, like a repair module that repairs ships something like 1 hp a turn.  And maybe a training module that increases ship XP gain...

@ Astax:

Actually, I think it may be possible to mod your initial colony upgrade idea into GalCiv2 (though it would still be interesting in GalCiv3).  In fact, that's on my list of things to do anyway.  But, we'll see.

I'm already out of ideas, but, if anyone wants to make a post to where you give karma (to who responds and give it around) in just a single post, do it, I want lotsa karma, only cause I got one cause someone thought I was crazy, he never responded why.

I know, i was just seeing if anyone would fall for it.