The UI has bothered me for quite a while. However, until now I havent stopped to think what was the problem. Here is a few ideas I have in no particular order.
TOO MUCH CLUTTER
The Sins of the Solar empire unit display is growing on me. However, it also clogs up a ton of screen real estate. I think a few right click menu options to allow you to configure this on the fly would help. Such as being able to turn off one of the notification types, allow grouping the cities by city types, and also see armies that are inside cities. Personally I would remove the city listings from the left side but thats just me.
Important Notification Area
The notifications on the top right require multiple clicks to close. When you close all the notifications under a category the category should automatically clear. Also I think the icons need some work to make them flashier or more colors. It is really easy to miss because they basically black and white. I know this is moddable and I consider making a mod for this.
End Turn Button
Every strategy game should steal the reminders from Civ 5. For those that don't know. Civ 5 forces you to give orders to all your units, assign production and set your research before you are allowed to hit end turn. This is a great help for newer players by teaching them the mental checklist (totally stole this from Day9). In my opinion this is one of the most innovative design choices the 4x genre has seen for some time and one of the easiest to implement.