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'.