One thing I would like to see are support Ships.
Combination of spacedocks for repairs, stores for rearming and refineries for refuel to allow fleets do deep strike and raids.
I'd love to see cargo ships move between systems, not only it would add some immersion, but also allow raiding warfare and the need to protect your "supply lines"
Yes, I know that you guys probably don't want too complex a logistic system, and I don't want it either, but some sort of logistics would add options and those are almost always good.
Another issue would be to find some sort of role for lesser ships, as in patrol and escorts, a lot 4X tend towards massive battlefleets of super dreadnoughts, and a fleet is more than its battleline, actually looking at wet navies there are a lot of roles for smaller ships that need be done, with only size progression, it simplifies warfare into batter enemy fleet, reduce defenses, invade, rinse and repeat.
You either win the war from the get go or lose it with very rare exceptions in most 4Xs.
Honestly, while nowhere near the game, Distant worlds addressed some of those issues and while Distant worlds is a difficult game with too much logistics and the like, some of the ideas presented in there were very interesting (the need for escort ships, the importance of a civilian economy, the possibility of inflicting the death of a thousand cuts against an enemy and other asymmetric forms of warfare, etc)