Nice idea, but if you start offering different rates per aircraft, you'll fill the more efficient ones and then run out of available aircraft to operate.

Say you offer 6 flights to JFK with a 747 and 1 with a 777, you'll fill up the 777 leaving the 747 flights with less people. Given that the 747 aircraft still have to operate, I'm not sure what savings will be made. Also, you can't just swap aircraft around too often, since capacities are not the same for all aircraft and there are only a limited number of aircraft available.

I do like the idea though, if only someone could work out how to make it work in practice!