I'm not so much for developing new bikes as I am for developing an environment for creativity in motorcycle development.
I would think that the FIM and AMA should create a box class (anything goes as long as it fits in this box) with very simple rules for safety and for aiming the technology development in a particular direction. For instance, an class open to any technology, any capacity, any fuel, and weight. However, since the idea is developing "greener" equipment (and not Kawasaki Green

), there would be a limit on the amount of fuel you could use per moto as well as an emissions and sound test at the finish...for ALL participating bikes.
Then, although the factories could dump gazillions inot development, the little guy could come up with something smart and do well as well is the small factories (Can-Am, Bultaco, Maico, etc come to mind) might be able to beat the Big 5 due to economies of scale.