The user interface could be better still. I'm not saying it is worst than two, which it is not. I'm not saying some of it isn't awesome which it is. I'm talking about double clicking. I used to be able to double click on mercenaries to select them. I can't anymore. I pick the tech tree when I select a tech. I still can't double click on a tech when I know what tech I want to take it to the main screen. I can't double click on a improvement on the colony screen when I change my mind. I should be able to go on the square, or the build order to do this.
I could use a list of planets order by faction with their logo to find them. I'm thinking in particular traders to help prevent diplomatic incidents on the main screen.
On the ship list I use this to move my ships, and check my territory for monsters... Sometimes I build things, or plant colonies. When I do this my ship list start over. This is why this is a problem I can't memorise the names of all my ships when I'm just checking location. When you have 50+ ships this is impracticle for me. So if I have to find my previous location in the ship list this is impracticle. Instead go to the next ship instead. I'm talking about my place after I build something...
In two there were a list of events that happened. I used this when I had to remember what I did. In three this event list is missing. Now it would come in handy reporting bugs. Which brings me to my next point.
A bug I noticed seems to be affected by population. Is a choice will award a bonus to population, but it doesn't. If I knew it didn't I wouldn't select it, but since I cants check my events I can't figure out which event did this, so I can't report it either.
Ideologies benevolent is a synonym for good, while antogonist is one for evil. If you don't want to sound like ideologies then rename these, even if it would require you to change the abilities a little. Maybe four ideologies would look a little less like good vs. evil.
Can you add this as an option to bring in the jagged knife, order... As an option then the ones who don't like it can opt out. The jagged knife just couldn't manage it's planets, and the other ais didn't realise that there planets weren't taken. This needs fixing.