A few UI improvement suggestions:
Ship Design screens: allow right-click menu for filtering buttons, to bypass the dialogs. So changing for filtering from non-obsolete ships to non-obsolete units takes two clicks and small mouse movement, instead of three clicks, and much more mouse movement. Same for component filtering in the actual design window.
Cargo Transfer/Unit Launch/etc. screens: make the display collapsable. So if you have 100 sats in a group, and you aren't working with any particular satellite in the group, you can just collapse the group and have more screen space for anything else in the sector. This applies to the cargo/supplies/ordnance for individual items as well.
Treaty Negotiation: allow for this to collapse as well, so specific provisions do not appear until you select the higher-level provision it is under. For example, don't show the 5-30% in trade treaties until you select the Trade Percentage provision.
Systems/Planets/Colonies/Ships/Construction Queues screen: allow Layout and Filter buttons to have right-click menu access, to prevent needing to go through the dialog.
News Screen: Make a small view! While the pictures are pretty and all, I want to be able to see more than three news items at a time. And also, if a spaceyard constructs more than one item in a turn, put that all in one news report, instead of breaking them up into several.
Orders Buttons: it would be nice if the 18 orders buttons in the bottom right of the screen could be customized. So, in the early game, I could arrange it so the top six buttons are Move, Goto Waypoint, Colonize, Explore, Survey, and Resupply at Nearest, and arrange the other orders in customized submenu buttons. It would be even nicer if we could do this based on the context of what is selected, and save these layouts to distribute to others. Or... I could just start memorizing those hotkeys
System View: it would be nice to have the axis of rotation for panning be somewhere other than the center of the system. This one is completely pointless, really, it just makes things look cooler; you can set your camera over one of your colonies, and survey the system from that POV. Also, is there a way to turn off the hex grid? How about grid off, and keep the outer boundries for FOV? Also, clicking on a flag should highlight the sector the flag is attached to.
That's it for now, I'll probably come up with more later.