Hey, I hardly have a monopoly on hacks where you play as the villain. :P Just don't copy ToxicPurple's ideas and I won't have any problem with it.
I'd recommend you hack Ruby, though. Even though Sapphire and Ruby similar, there are enough differences that hacking tools configured to work for Ruby won't work as well for Sapphire, and when you do releases of the game a lot more people will have a Ruby rom they can apply the patch to than will have a Sapphire rom. They could probably find a Sapphire rom pretty easily, of course, but it's never a good idea to annoy people wanting to play your hack by making them have to download a whole new rom just for the purpose of playing your game, when every other hack out there is compatible with either FireRed, Ruby, or Emerald. I also wouldn't recommend hacking Emerald because I've heard that it's notoriously hard to work with.
Anyway, good luck with your hack! Getting to be a part of Team Aqua certainly sounds fun.