Ironclad/Stardock, a great game you guys have here. Overall, it's so far been a very cool experience. Here are my comments & suggestions based on my first-time play-through:
Gameplay Suggestions
1) Would be nice if a progress indicator of some sort was shown when colonizing a planet.
2) Would be nice if there was a retreat button for all ships (this could mean retreating to the nearest out of gravity well planet)
3) Unit groupings. Would be nice if I could have some sort of way to issue tactical moves such as (a) wait until all units are in the indicated gravity well before proceeding to the desired location; (b) formation order (e.g. optimal to which ship would best go first, and which are best last); (c) AI attack aggression levels (head straight for target vs. attack all in its way to its goal vs. avoid attack altogether)
4) Some sort of clickable map such as the one in GCII (the Empire Window (EW) does not do justice as to where the planets are relative to each other). Though one can zoom out to see some sort of 'map', it would be better if this was immediately available in the form of a map.
5) A minor thing: not sure how many people would feel this is a good idea but I think it'd be cool to have some sort of encyclopedia one could browse to see what are a certain unit's purpose, possible upgrades, etc.
UI Suggestions
1) Click dragging to select multiple units does not work if I start dragging from within an object's boundary box (be it a planet, factory, or ship).
2) Would be nice if the EW indicates what each of the ships are doing (e.g. Idle, moving, attacking, being attacked (for ships/objects that can't attack, etc.)
3) Would be nice if the EW either groups construction capable units in its own, additional section/subsection or if they are selectable from the fixed structures section. Too many times I have been unable to find where my construction unit was (the icons are way too small) and ended up simply clicking on the planet of interest from the EW instead.
4) An option to permanently show health bars and progress bars would be wonderful.
5) An option to keep info cards fixed until you close it like a pop-up when a single unit is selected would be nice. Right now I find I have to keep my mouse cursor on the desired unit at all times to read it...
6) Maybe make the research window collapseable such that a small part of it is shown with the rest of the screen showing the main game with the planets and ships and such.. would give the player time to ponder over what to research while doing other stuff.
Controls Suggestions
1) I find that when rotating the camera, the camera moves way too fast. It would be nice if I could also move the camera with the scroll wheel button as well by default. Also, would be nice if I could move the screen by say holding the left mouse button instead of having to move the mouse to the edge of the screen.