My suggestions:
1. Provide better feedback on the status of factories (working or idle). There is a little spark animation inside the factory when it's working, but that's actually pretty hard to see from a high camera angle, or when you are zoomed out. What you need is a more visible indicator, and one that carries over to the factory's icon (so that you can see which factories are working and which are idle by looking at the icon list on the left side of the screen). Perhaps you could have little flashing lights on top of the factory that are red when it's working and green when it's idle. This would translate to a little dot (green or red) next to the factory icon in the list and when the view is zoomed out. That way, you can easily see at a glance which factories are working and which ones are idle.
2. Similarly, it would be good to have the same sort of feedback for research. IIRC, there is a voice notification when you finish researching something, but there is no indication (short of opening the research window) of whether or not your researchers are currently working or idle. Since you can queue up multiple research projects, it would be handy to have some indication for when the queue is empty, like a little red or green light/dot on (or next to) the button that opens the research screen (if you went with the same system for factories, that would keep everything consistent).
3. Some of the icons are hard to see against some backdrops. In my current game, I'm the orange player and the "space" color is orange, which makes it very difficult to see my empire markers over planets. Zoomed-out ship icons are easier to see, probably because they have a dark outline and some dark shading in them (the empire markers are just flat orange). Even those, though, could use a little more contrast.
4. Furthermore, a lot of the ship/structure icons look very similar to each other and are hard to tell apart, especially at high resolutions (and double especially against a space backdrop that is the same color as the icons). My advice would be to make them simpler--perhaps more of a flat, iconic affair (like the empire markers over the planets, with a drop shadow or outline to make them pop against a similar-colored backdrop) rather than the detailed, two-color renderings that you have now. At 1600x1200, it's impossible to distinguish much of that detail anyway--it just makes the icons harder to read.
Here's a touched-up screenshot, to illustrate:
I really like what I see so far, though. This game has lots of promise--keep up the good work!
