As stated above in my post i did wrote '1 legendary of your choice per account ' which means there wont be a team which consist of all legends and make them rares so that they won't be seen often in a team as they would be like you said, broken
Implement a rule/conditions where an account is only allowed to have 1 permanent legendary which they ofc have to catch one themselves. For example I choose to catch a Kyogre then I can go to a special designated place (or you guys can make it so that they could spawn in randomly maybe) and if I did catch the Kyogre then I would not be able to catch any other legend and have them in my party/pc permanently and probably increase the rarity so they won't be seen often