If they were to go the route of replacing Transformers with Pokemon at USH, It would obviously not would be the exact same ride USJ is getting as Transformers is two levels and Spiderman is one, plus with MK being right next door it wouldn't make sense to have an almost identical ride literally right next to it
What I could see for a Pokemon overlay for USH's Transformers would be to upgrade to the next gen SCOOPs on USB's JW ride, ditch the 3D glasses, and add in some form of interactivity.