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Because OP is being a faggot as always, I'll take a crack at how to actually fix overleveling, even though that's something Gamefreak actively wants to encourage because Gamefreak is fucking retarded.
A built in level cap.
Badges now function much differently, they are now synched to Pokeballs in the same way they are to Pokemarts, if you do not have a certain amount of badges, Pokemon will not level up past a certain point, they will not gain exp just like how a Level 100 Pokemon wouldn't, if you can't buy Full Restores with the Thunder Badge, you shouldn't have Pokemon past the level cap.
In addition to this, you cannot use Pokemon that are above the level cap, if you somehow encounter a Pokemon that is above the level cap, you can still catch them, but you can't use them until you have enough badges, they will be sent to the PC even if you have an empty slot in your party, this also applies to overleveled Pokemon acquired in any kind of trade.
Just to make sure you won't be overleveled at all in the maingame, the level cap will only be disabled once you enter the Hall of Fame, all battles will be properly scaled to the amount of badges you have.
THERE. WAS IT THAT. FUCKING. HARD?
NO. IT WASN'T.
I THOUGHT THAT UP IN UNDER AN HOUR.
