There are a couple things that I think could be improved and would help those playing (as I do) on very big galaxies.
1. In my current game I tried doing the Dread Lords challenge. I was careful not to attack more than one Revenge fleet at a time, but that wasn't the problem. The Dread Lords fleets are colored red, while other factions have fleets, etc. colored red, orange, etc. This made locating the fleets rather tiresome. Not a huge problem but I think unnecessary.
2. When trying to find trading partners to obtain certain strategic resources (which I was doing when trying for certain prestige challenges), when there are 20+ other factions in the game, it's a bit of a chore to check each one to see if maybe they have helios ore, for example. I think this could be streamlined --- for instance by selecting something you want (resource, tech, whatever) and clicking a button to show which factions if any have some. This would save a lot of hunting and pecking, perhaps.
Minor issues really to improve the ratio of 'fun time' to 'busy work time'.