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In games like Pokemon Stadium 1 & 2, the legendary birds and the legendary dogs could be used in normal tournaments, but Pokemon like Mewtwo, Mew, Lugia, Ho-oh, and Celebi were out-right banned. Nowadays, even pseudo-legendaries like Garchomp are nearly banned from certain online battles.

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It's not written anywhere how they decide on what Pokemon got banned but they test them. A Pokemon might have a high attack stat but have other stats sub-par.
Look at Moltres and Mewtwo for example, they are both legendary but Mewtwo is banned while Moltres isn't.
Mewtwo's BST(Base Stat Total) is higher by 100, standing at 680, while Moltres' BST is only 580.
Moltres does have 100 base attack and 125 base special attack but it's slower and has lower defense stats than a lot of Pokemon used in higher tiers, outclassing Moltres easily.

That being said, the BST might make the Pokemon appear weaker than it actually is.

So the answer to your question would probably be the BST mostly decides what tier a Pokemon is going to be, alongside with its overall performance.

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I guess banning Phione (a Pokemon that no one even wants in a trade) is pointless. Its not like the thing has an unfair advantage over other Pokemon. If anything, it's the Magikarp of legendary Pokemon who's unfairly disadvantaged over all the competitive regulars.

But still, I wonder if such rules even apply in the anime. I wonder if everyone would freak out if Mewtwo entered the battlefield (as if King Piccolo stormed the place).
Ehh, but wasn't Darkrai enough!?
Excadrill is legendary then 530bst
So in the anime I guess no Pokemon are explicitly banned (since not two many people even see, let alone own legendaries to begin with, and not-so-everyday legendaries and mythicals can be branded as legal or illegal by Pokemon League officials. So its okay for Ash to use a Pokemon like Keldeo against a Reshiram. Only the real-life meta-gamers would complain.