I'd never even reach that stage.
I would firmly refuse to catch anything more than 6 pokemon, because I would feel guilty of knowing that I would either have to store some (AKA, abandon them, and leave them completely alone) or release them, after I had created a bond with them, wich is kind of a dick thing to do.
Soo, I just created an "elite" team of six pokemon that I liked, and trained them really well, so they massacred all the opposition the encountered in the story, without real effort.
I've had a period where I felt really bad for "killing" wild pokemon, but after a while I found out what the english word "faint" meant, and that they later just woke up, and chew berries to get better again.
Then I went and murdered team magma, and team aqua, and stuff...