I snuck Latios and Manphy in but dont know how
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Some legendary Pokemon can't enter.
no, there is no way to make legendarys shiny or any Pokemon shiny but there is a way to clone them in battle tower.
Palkia is not qualified to enter the battle tower tournament, this rule remains unchanged to all legendary Pokemon except pseudo-legendary Pokemon such as Articuno, Zapdos, Moltres, Entei, Raikou, Suicune, Regirock, Registeel, Regice, Latios, Latias, Mesprit, Uxie, Azelf, and Cresselia. All others are not permitted to enter.
the legendary Pokemon are different levels when you catch them. also in crystal there is a battle tower where when you beat it you can catch suicune without a masterball because you can battle him without him running away.
The non cool thing about the battle frontier is you can't enter legendary Pokemon however you can go around that rule by having the following Pokemon: Regice, Registeel, Regirock, Articuno, Zapdos, Moltres, Raikou, Suicune, Entei, Latios, Latias. For some reason those are the only exceptions to the rule of legendary Pokemon maybe because the rest of the legendaries are overly powerful.