I think it would be very interesting to have a nonlinear game, somewhat similar to the play style of Mass Effect. I mean this in terms of being able to travel from planet to planet and explore them. THis game would be without a leveling system though, so no RPG level progression or stats. The game could be third or first person on foot, but I think first person would be more interesting.) It could have a major story, which would involve STF and whatnot, and it MUST have some GINORMOUS battles. But there would be plenty of side quests, like SKyrim. You could respond to distress signals, engage in commerce, fight off pirates (or pirate yourself) etc... I'm not sure if ship combat could be done well in fisrt, so perhaps third person for ship combat. You start off in STF as a lowly officer, and advance to admiral, giving Starfleet itself orders and conduct diplomacy and start wars. (the AI would control everything but yourself and your own ship) Or perhaps you could become an extremely notorious pirate or mercenary.
Because leveling complicates things too much for people like me. I used to like complicated games. But I've grown ultra tired of hard learning curves. I had having to make 'builds' 'just right.' When I come home I wanna have fun, not do more work. Not that leveling, configuring and grinding isn't necessarily unfun, but for me and people who don't have enormous amounts of time to spend it's not good. This would be game is only single player or co-op. Going back to what I said. You could command Starfleet yourself, give orders and whatnot. A battle could be completely fought by the ai following your orders to fight. You could also be an Admiral which gives tactical orders during a battle, or just a high up guy who tells the fleet to engage and an ai admiral does that instead. (I am a huge NPC enthusiast.)