I think the movie would've been better as a Starfleet vs. Starfleet drama and completely removing the S'ona from the film.
I like that idea. If nothing else, it would've removed a lot of the plot holes about the whole Baku-Son'a thing.(like how did the Baku kick them off planet? Why didn't the Son'a settle somewhere else in the intervening years? Don't they have an equal right to the planet? etc.)
Actually yeah, your idea makes for a smarter and better movie.