I think the different cc and cylinder rules are good to allow for more manufactures to participate and be competitive. It also gives the engineering depts a challenge to see who can build the best and most competitive engine and chassis package with the option of cylinder and cc configs.
If this isn't an option and it's all 1000cc we would loose out as the consumer in the long run as there would be no need to keep pushing the engineering envelope for some of these engine types.
So, Ducati, MV, and Triumph wouldn't have production based race bikes or they would be just like all the others and we would have choice of color and name on the side. Then it would be 3 different cc sizes of the KTM RC390 cup and just a rider battle. That would get boring... Just my 2 cents.