That doesn't mean they're not a whole lot better. If the opponents couldn't use uber-legendaries, then you roflstomp them with Kyogre Palkia Arceus etc. If they could use them, then you would also have to use them to compete. Banning certain legends keeps the Battle Subway from being broken, and actually expands your catalogue of useable Pokémon.
...Battle Subway....NOT broken as it is?
Brokenness is relative. --- Why do I have to move with the crowd of kids that hardly notice I'm around? I work myself to death just to fit in.