Good shit so far. Here's my contribution that my dumb ass forgot to include in the OP: Wild Pokemon boss battles.
Not like Totem Pokemon where they're super-powered big fellas, I mean just regular ol' wild Pokemon that're pissed off and overleveled. They can be optional and blocking off certain areas with goodies, or required by the story.
One such example could be a couple of rivals accidentally pissing off an Ursaring by dicking around in its territory or something, and they use you as a meat shield while you tussle the fucking thing.
For added effect, these battles could have slow, heavy music fitting for a single, powerful Pokemon, something like this:
https://youtu.be/nNsx4Mm3jSA 
