Nintendo is the sole owner of the Pokémon trademark, but a separate company was created to handle licensing deals called
The Pokémon Company, which is made up of Nintendo, Creatures, and Game Freak.
If Nintendo wanted Pokemon in the parks, they could arrange for it to happen... and I'm sure the other two parties wouldn't mind the added merchandise sales it would drive.
I have no idea about structural issues at the amphitheater, but I'm an advocate of tearing it down for a new family style dark ride any day, whether it's Secret Life of Pets, Pokemon or even
Heathcliff, I'd love to see something open up on that long stretch of nothing.