Because that is where Bryan Fuller wanted to tell his story.
Considering how little of Fuller's vision we actually ever saw (original tri-colored uniforms), and they pretty much kicked him and everything he wrote out.... the only true reason we're stuck in the prequel setting actually seems to be that they started halfway there, and didn't have the balls to cange that untill their self-set release date...
This is one of those instances where you have to wonder what they were thinking in the first place: Just WHY agree to Fuller's idea of a prequel setting, if none of the money guys actually wanted to do a true prequel setting?