I hope to collect some ideas about how to polish the UI in this thread. I will start with:
In the left-hand LOD (is that correct term for the icons on the sides of the screen?) it would be really nice to gray out those units which have no more moves left. There is no indication for that right now.
I hate it how the game does multiple things at the same time. It is possible that the technology screen pops up, and at the same time you are attacked by monsters. So, the technology screen auto-closes, and if you don't remember to pick manually a new technology to research after battle, you are researching nothing.
Quests: when you get the pop-up "attack guards / flee", first: always have the "flee" option as last one. More consistent that way. Second, show what you are facing (like in the normal battle start screen), so that is is not pure guess work or learned-through experience based decision.
Is there a cheat-sheet of all the hotkeys somewhere? I didn't spot one. How do you see the "settle" values without using a pioneer.
F3 brings up some debugging stuff.