Hey beautiful Modlies, sorry to add on to your work load, but could you possibly help some one new to apping Pokemon characters to a game?

Mainly I'm concerned about Mr. Mouthbreather N here still having Zekrom and Zoroark during his canon point. How do y'all handle a character dragging Legendaries around, especially when it comes to some one who would probably want to have them out of their Pokeballs more often than not?