First off, let me start by saying this has to be one of--if not the--greatest games I've ever played. I'm sure that's probably a cliche around here, but you guys hit the mark for me. Good job
That being said, I don't think I'd feel proper without adding my own list of things I'd like to see to the mix around here. I've got a few in mind off hand, and I'll probably come back later and add more (I know I've thought of more in the past that escape me at the moment.) I was thinking of putting these in the version 1.3 wish list, but some of the stuff I'd like to see might be a bit more appropriate in a full version change (i.e. 2.0, or GCIII.) In hopes not everyone is tired of this stuff...
1) Do Something with Unused Tech Points. I haven't completed a game and gotten an actual score yet (never enough time, and I can't figure out what I was doing when I reload a saved game), so maybe there's extra points for not using all the tech points on a race at the beginning. If that's the case, great. I would like to see something done with them though, maybe having the ability points and the tech points pooled together--some days it'd be nice to start a game without any ability points but maybe an extra tech, some days the opposite.
2) Allow In-Game Custom Races to be AI Controlled. This was a bug in the 1.2 B1 release I believe, and I didn't run across it myself. But others on the forum mentioned it and it sounded interesting enough, basically having a modded game without modding it. If this were allowed, I'd recommend also allowing for more than one custom race to be played at a time, so the user can play one against another. You could have the AI for the race randomly picked out of the existing AI profiles, or randomly generated (if your AI model would allow for something like that.)
3) More Detailed Modding System. I know someone's probably going to get on to me about that one, but I really only have one thing in mind and didn't know how else to put it. I finally worked up the nerve to try my hand at creating a mod, and came up with some tech and improvement ideas that probably would've been pretty killer: an arms factory to improve military production for a planet, a social factory to improve social production, and star base modules to add to the individual production levels of nearby planets. Of course, as soon as I looked through the modding guide by Cari, I found out that it just wasn't going to happen. There may be some work around I'm sure, like an improvement that affects the base values, but no quick fix. As I said, that was my first attempt at modding so I may have missed something; also, I may add to this part later as I try again.
One last thing, which is more of a question than a suggestion. Have you guys considered possibly either releasing the game as open source (but not free--I'm sure there's something that could be done) or releasing some kind of plugin/SDK to allow other developers to add on to the game? I know open source may be out of the question, but it could also make things a lot easier for you (someone fixes a bug and sends you the patch instead of a forum thread of 200 posts trying to debug something.) You guys don't seem terribly concerned with piracy based on the lack of copy protection, and I think someone going through all the trouble to get the code and set up an IDE to build it just to rip you off is much less likely than someone who'd spend less time just to find a torrent for it.
Just some thoughts; like I said, I might add to this later as I remember things I can't think of now.