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The thing about pokemon is that most boss battles are turn based 1v1, so they can't just make a legendary too powerfull because it will leave your pokemon completely helpless against it. Especially if the legendary happens to be faster.
Other kind of games don't have this problem because they are either non-turn based or you usually have control of at least 3 characters during battles. So when facing an overpowered boss, you have a bigger variety of strategies to use, like putting the character who can't hit as hard in the back row as a healer/supporter while the other two attack the enemy.
Pokemon already has doubles and triples battle, so there's a possibility something like that will be implemented sometime in the future (well, it kind of already was in Collosseum and Gale of Darkness, but I'm talking about main series games), but I wouldn't count on it, since they haven't changed the 1v1 system not even after adopting doubles as the official competitive format and deliberatedly balancing the game towards that mode.
