Indeed, regardless of where a character hails from and how powerful it is in there, it should be balanced for MUGEN. Sure, if a Pokémon (let's say Steelix, for example) excels in a certain stat (defense) and isn't as good in another (attack), you'd make the attack lower than average and its defence higher than average, but not so much that it's too weak/game-breaking.
This is why Cyberlizard's old Rayquaza is so cheap - its attack is so high to represent its 150 base attack in the games, but it doesn't fit balance-wise into MUGEN.