First of all, the game works great on my computer, Pentium D 3.0 Ghz, 2 GB RAM, x1900xtx. 1680x1050 res. Haven't had any massive battles with lots of AIs to see if I can strain my machine because a huge game would take days.
1) The UI is missing a minimap. Okay maybe you don't want a minimap and want me to zoom around, ok. Consider this, in my first game I kept hearing the pirates launched thing but never saw any pirates and eventually one day I check out one of my far away planets and it's covered in pirates and most structures blown up, hmm wish I could have seen that sooner. Maybe a easy way to zoom in on important events, I dunno.
2) The sidebar list. I don't care how many extractors or research stations I have on a planet. I need to find my factories fast so I can change way points and issue construction orders on the fly.
3) I need the buy/sell metal and crystal buttons on my main screen. I buy/sell a lot and all good players will.
4) I'm not sure how many capital ships are supposed to be in a normal game but how about a zoom and select nearest capital and have that button rotate through them all.
4.1) When something is being researched, replace the research icon with a progress bar + name of what is being researched.
4.2) Change resource icons to 1000 (+7.5/s) If I want to hover and see the breakdown, okay.
4.3) Play around with the location of the hover info box. Right now it's in the lower right hand corner where it doesn't really catch my eye. Maybe it's just me or my 22" widescreen monitor

Gameplay:
5) Game is way too slow. I like a long game, but sometimes I find myself with nothing to do. 2hrs for a tiny map that you don't even go through 1/3rd of the tech tree is not right.
6) Colony ships. Can we get rid of these please? It's useless micromanaging and since there is no penalty for having a bajillion planets, there is no reason not to colonize everything. Make it so the pop goes to 0 and then if I have a majority military presence in the area, the planet shifts to my control after a set amount of time.
7) Tech tree. Stuff takes a lot of research centers. The amount of centers needed for technology should be scaled based on the size of the map. I find in 1v1 and 2v2 maps I can never get very far into the tech tree.
8) Cobalt rush. This is what I do, what the AI does and is sound strategy. The thing is that building a research center + researching a tech costs as much as building maybe 5-7 cobalts. There is no real replacement to the Cobalt so a boom strategy has nothing to shoot for to counter a Cobalt rush. In order words I would like MOAR UNITZ!
9) Siege ships. These ships are dumb, charging stright into a planet to kill it. These ships also have only one purpose which kinda makes it lame. These ships should be able to damage other ships, maybe give them splash damage as well, like land based artillery. Current system is, clear a path, them pahse in siege and guard them. Hardly interesting or fun.
10) Formations? I dunno, ships just overlap each other and if not zoomed in, 3 ships could actually be a cluster of 7 ships.
11) Counters. Most good strategy games have counter units. As it stands now, having more units + more tech will win me the battle guaranteed. And by more units I mean more quality units, of course 3 cobalts will die to 2 capitals. If a 10 Cobalt + the starter Capital comes at you, what is your counter?
12) Focus fire penalty, bonus for attacking a ship at it's side or rear. More ships, more hotkeys, more weapons, more races, more options, more maps, more booms.
Conclusion: This game gave me happy goosebumps in that it could be really fun.