I don't see anything wrong with using legendaries as long as they aren't in battles with other people. In game I think it's fine, especially if you like a legendary pokemon.
I had a Rapidash, but he kinda sucked, so I switched him out for Dialga because I wanted to transfer pokemon over and get the ELite four over with.
All my pokemon were either high 40s or low 50s when I beat the Elite Four.
Cheese (Pachirisu)
Victoria (Weavile)
Don Rose (Roserade)
Dialga
Arthur (Empoleon)
Twila (Staravia)