Simply because it cost as much to run a 250 gp team as a MotoGP team, just the bikes were not available in the big class. The cost of the 250 strokers were killing the class, and there was no innovation in engines - where were the rotries, turbo 4S etc - no, prototype racing quickly evolves to lookie likie racing as pretty much one tool does the job best. The control engine along with the control tyres gives free rein to the chassis guys. The new replacement for 125s as a single class could reduce the cost of prototype engines - but they will quickly all be the same.
Have to agree that there should be a different classification - say a 50 mpg class, a 25 mpg class and a 10 mpg class, where the limit is based on the fuel capacity and the race distance
R