Bringing the Thunder
I would prefer PrinceOfFacade's method to scaling wild pokémon with badges or your own party. Let players wipe if they go into high-level areas too soon if they fail to run, it's not like it's the end of the world if players wipe a couple of times. They'll learn not to go there until their pokémon are stronger. I would have even pokémon you're the OT of not obeying you unless you've got sufficient badges though, otherwise it'd be too easy to simply go into the high-level area, catch a few pokémon there, and essentially skip levelling.
An anecdote, I once played a Nuzlocke in the Johto games and managed to catch Raikou not long after reaching Ecruteak City. It was an amazingly lucky catch, but it did pretty much break the game as it was so OP for that stage in the game. Raikou, Entei, and Suicune being so difficult to catch in those games balances it out a bit, but you don't really have that luxury for regular wild pokémon.
Game Freak isn't going to go for that. They want the game to be accessible to kids and casuals, they're not going to let them get frustrated because they get massacred going where they want to go. Also sort of defeats the purpose of open world if certain paths are tougher than others.
Honestly the closest thing we'll get to an open world game is Pokemon Go because we can go anywhere in the real world to catch the critters.
Pokemon Go doesn't really scratch the itch to explore large virtual worlds, which is the problem. If I wanted to explore the real world I wouldn't need to buy a video game.