From some of the features I have read and how SF plays in general, I get a lot of Starfleet Command (I,II,III) feelings here.
One thing I would really like to see and what I think also would fit nicely is the SFC III's 'galactic open game' play where you have a huge map of hexes, each representing a system or open space or nebula or whatever. You could move between them and each one offered a mission, randomly created from a set group of predefined or dynamic (face-off style) missions. Each would give you prestige and with that you could acquire new ships, ammo/shuttles and crew members at starbases/planets.
Only thing I was missing in the game were negative aspects. F.i. your crew personnel, no matter how badly your ship got blasted, never died. I would always add in some criticals (the tabletop game StarFleetBattles, from which the game originated, did have this iirc) where something additional might break or you could lose a crew member.
They also never transferred or retire or anything.
Then again, they also did not have special skills. Think of it as RPG style item bonus. Bob has +1 to weapon accuracy, but Sally has +1 to damage, who you gonna chose as weapons officer?
Anyway, this is not a demand list, just some ideas. I gladly leave everything up to the devs and will be happy with whatever direction they chose to go.