Yes, I forgot to add the balance between low/high-tech units. I outlined the problems with these a few posts up ^^ And there's also an issue with planetary defenses being too weak, especially the low tech versions. Rather, not so much "weak" as "waste of labor". If we don't increase their halfLife they could still stand to be buffed somehow. Same with citadels. The "somehow" is the difficult part.
Personally the feature I'm looking forward to the most would be the different empire colors. Shouldn't be too complicated a change, I posted a bit about how the source JS defines colors, all we would need to do is add a "neutral" color as opposed to only "player empire" and "enemy". Replacing the placeholder grey boxes would be a very nice visual change too, I agree. I'm sure some Transcendence ship images can be used in place. Heck, IIRC there's an "Eldritch-class" and "Minotaur-class" in the Eternity Port expansion already!
One last thing: Fleet Icons.
The fleet icon colors would need to be changed as well if we're having different empire colors (should be another easy change that improves the game a lot). Right now there's only yellow for player fleets and red for everyone else. Something better might be green for player, yellow for neutral and red for enemy. Blue can be another color if an "allied" state is introduced in a future update.
Something like this (from my current Stellaris playthrough). Look how pretty the galaxy is. Oh, and each fleet type has a different icon - combat, transport, explorer and constructor vessels can be distinguished clearly. Something else that can be