Ever notice the huge hump on the passenger side of the floor board? That is where the factory pipe and cat goes. I've heard of a few people running two pipes along that area, but it just seem like a lot more trouble than it's worth.
Again I will say that you can flow just as much air (within 8%) through a 3" pipe than you can with two 2 1/4" pipes, and one 3.5" pipe will flow the same as two 2 1/2" pipes.
I don't know if you can get a 3.5" pipe to route over the axle with no clearance problems, but I do know that if you can, it'll add a lot less weight to your car than two 2.5" pipes will.
AJ