Initial thoughts
I just played through my first game of GalCiv III Alpha. Despite the "This will not be fun" warning at the beginning, I found it very enjoyable. Obviously pared down and simplified, but it ran smoothly and there were no obvious game-breaking bugs. So here are my thoughts on what could be improved. Again, this is after my first game and there are no tutorials or tips in the game yet, so I apologize if I list something that is in the game, but I couldn't find it:
1) I don't like the way the single button on the bottom right hand guides me through my turn. In a game like this, I want more control over exactly what I am addressing and in what order. I'd much rather have a list of things that need to be addressed that I can view and deal with in the order I choose. Maybe I want to do some scouting with my ships and see what kinds of weapons my enemies are using before I choose my next tech, etc. There are some workarounds, but it felt clumsy to do anything but address the issues in the order the button brought them up. I'd much prefer collapsible menus from which I can view all of the issues at once and choose which to address. The botton also was part of the only real bug I encountered: it took me to a fleet that was without orders, but had no movement points left. I couldn't do anything with the fleet, but also could not get the button to switch to another unit or to end the turn. I can't remember exactly how I ended up resolving it, but I finally got the game to recognize that I didn't need to do anything more with that unit. The bug itself was a minor one of the kind that often slips into a finished game, but because the button won't let me end my turn until everything has been dealt with, if I hadn't been able to resolve the issue I would not have been able to continue that game.
2) Need an alert when ships are done. Simple and straightforward, I'm hoping this is already in the game, just didn't make it into alpha.
3) I don't like the UI for research. Because it is just a list it is hard to think about the tech in terms of what you've already researched and what your research is leading toward. I really like to be able to see the actual tree it helps to visualize the progression aspect of research. The UI for this in FE works very well. If you don't want people looking way down the tree to pick what the research now, then make a tree that only shows those tech that can currently be researched, or those and the techs they lead to.
I hope these are helpful to you as you try to make GalCiv III as good as possible.