A cell-shaded RTS that is heavily story-based would be interesting. It would be rather forced to be after JJ2, since before JJ1 as far as I know the rabbits and turtles were at peace. However, I don't think that there could be a third side without one coming out of the blue, and generally to have enough variation a RTS needs at least three sides.

EDIT- Why did you put a grey background behind the white text? That makes it really hard to read.