City icons
The city images in the empire tree are all the same (I think they change based on city level, or maybe faction, I can't really tell — most of the time they are the same). By the time there are >4 cities in play, those icons might as well not exist since I can't remember which one is which past the first few.
Suggestion: replace city images in the empire tree with symbolic icons representing the type of city and its level. "My huge conclave city" is much more memorable than "my third city". Using standard faction crests (circle, square, shield, star) with the faction flag and a roman number inside, for example, would be a huge usability improvement.
Army icons
These could really be bigger. Unless the hero portrait is particularly distinctive, they are pretty hard to tell apart, and also hard to tell apart from hero-less armies. Army icons don't have to be the same size as city icons; in fact, there are usually more cities than armies so it makes sense to use larger army icons and smaller city icons.
The new colour-coding of unit types is great, but I can never remember which is which. Is purple a hero, or was that red? This may have something to do with the fact that the colours don't seem to follow a hue progression based on the unit's importance.
Suggestion: purple->red->yellow->green for sovereign->hero->unit->pioneer makes more sense than purple->yellow->red->green.
Suggestion: use shapes in addition to colours. The army portrait, in addition to being bigger, could be placed in a shaped frame (star for the sovereign, shield for a hero, circle for a hero-less army, square for a non-combat unit) and the small coloured dots next to armies and cities could use the same convention.