The cool thing about the piranha story is there are no real limitations on what can be done....as proven by the original sequel. Peoples expectations would be cheese, boobs, mayhem and mass destruction. So it'd be pretty hard to completely fuck it up.
I'd say they'd probly look at the genetic mutation side of things for the military or terrorists. A common plot, but one they could have a lot of creative fun with as far as the fish go.