Currently you can only choose between Klingon and Federation. Why not have an independant group for those who may not want to relate to either? Also, perhaps allow player created systems, or have a sector where it's freegame, where as a player who may play as a pirate can freely attack and pirate other players. Have a couple sectors (or maybe subsectors?) set up for this. Perhaps to draw in players is to also put rare items that can only be found in these sectors. Just an idea.
OP is asking that Cryptic's theme-park MMO be turned into a sand-box MMO. But I don't think that Cryptic can do sand-box MMOs with their game engine, staffing levels and general game-building experience. They specialize in theme-park MMOs.
If you want to wrap your head around some boundaries or limitations, look at the other games made by Cryptic Studios - CoH, CoV and moreso CO and then re-think your ideas with those games in mind. Oh, and don't forget the Foundry which is a shared resource with Cryptic newest MMO - Neverwinter.