heres my list:
1) frigates are almost fodder more than firepower, I often find myself using the scouts and the flaks for taking down capital ships and frigs, not a pretty, or efficient sight to see.
2) planets are far too small, I understand that theres a certain point that making them too big is an issue, but they dont need to be the size of beachballs
3) fighters and bombers like to fly through things rather than go through empty space (probably a tech issue, but I'm too lazy to move it

)
4) the nebula contrast the color of the host star. perhaps its just a taste issue, but I think its more pleasing to have a blue star on a black/dark nebula, a red/orange/yellow star on a red/orange/yellow nebula and a green nebula on a green nebula. its too wierd to see a red star in a green background...
5) the star's GWs are the size of dead asteroids. thats a big no no, if anything stars should be the grandmomas of all fighting zones. their gravity wells should be proportionately H U G E.
6) already been mentioned, but the way planets are tied together is freekish. they need to be more uniformly spread out and you shouldnt have to go away from a planet in order to get to it. (although I like the choke points, strategically useful)
7) AI is too figity, it will jump away if I so much as apply a little pressure to its kol battleship
8) AI is too tunnelminded, it will jump through any amount of planets just to get to one it wants.
9) a tad more cinematica. for instance the gauss cannon platforms should recoil, thats a really nice touch (and hopefully not too taxing, I dont know though)
10) the third dimension is ominously missing... its almost as if it never existed...
or maybe the devs didnt let us have it (30 Rock reference)
11) The Solar Systems when over 10 (yes, I modded it so that may be the issue) they make themselves uniformly arranged around a center Solar System, that makes things... odd, to say the least.
12) planets and solar systems are not arranged in the
third dimension... just a tangent off another point, but still, would be nice for them to be slightly off-kilter.
13) great opening gameplay, but the mid-late game is weak. I often find myself starting up new games rather than continuing old ones. this can easily be fixed by making later researches or artifacts have wacky or significant upgrades (new buildings or ships, perhaps a single-shot long RC missile silo on the asteroid etc. do wacky things to stars)
14) stars are not center! they should be IMO. they should provide something that makes them more important than simply the staging ground/entry point for an offense on/defense of your solar system
15) only one entry into a solar system! this makes turtling late-game too too easy. there needs to be some sort of specialty ability/ship or taxing capacity to leave and enter solar systems outside the star.
16) turtling... too too easy, and I'm a personal fan of the strategy.
17) AI should be a bit more agressive IMO.
now, this is a lot. I've got no delusions about that. additionally people will probably not agree with the majority of it, thats fine. but this is the stuff the devs need to pay a little attention to IMMITYO. (in my more-important-than-your opinion

)