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The thing here is that 3D doesn't allow the games to be abstract like they were in 2D.
When you played a 2D game, of course everything wasn't to scale. You didn't think about that. Everything is an abstraction of what it's supposed to represent. That's why you could have following Pokemon following you behind because the move was set on tiles and it didn't look weird. You could have NPCs just flipping in all 4 directions and stuff. You could have them just standing in the middle of a route waiting to battle and shit.
Now jump into 3D. You can't have that "abstraction" anymore because thanks to 3D you're starting to take everything at face value. Everything starts looking to scale, and everything starts looking silly because it's not an abstraction anymore.
It's an uncanny valley with NPCs just awkwardly standing up in the middle of a route staring forwards and then challenging you. Awkwardly Pokemon following you because now they're (mostly) to scale and it'd look silly to have a Slugma catching up with you as you run.
Pokemon games are 3D now, but they still feel like they're 2D games. That's the main problem these games have. Why they give that awkward sensation. Because all the elements that worked in 2D don't translate well to 3D.
