What I like compared to BotE:
1) Moons and asteroids.
2) In-game encyclopedia.

Production
1) There is no ship building queue, which increases micromanagement.
2) Right arrow on production screen doesn't work, only clicking on empty box increases production in the given field.
3) Unfulfilled requirements should be somehow marked (red font color).

UI
1) Tooltips would be very useful!
2) Main menu should be brought up in a more intuitive way than right clicking in the corner of the screen.
3) There should be an option to turn off galaxy map background, which is static and more than a little confusing.
4) Clicking on a line in summary should bring me to the system in question.

General
1) How do I get more Duranium?

Someone that played BOTF will have a headstart understanding the Supremacy UI.

Hehe, a small typo that makes a big difference.

I find the BotF UI to be too dark, heavy and somewhat convoluted. I appreciate the attempt to give it an empire-specific flavor, but for me it gets too tiresome after some time playing. And I really dislike the starmap.
I don't find tactical combat to be easy to handle either.