Giovanni, the leader of Team Rocket. The most notorious evil team in history. Was a Gym Leader. Mentor role doesn't have anything to do with it. He's still considered a Gym Leader with B2W2's tournament. Evil can be a Gym they just never bothered to make it.
I guess he was the only exception as far as Gym Leaders in general go, but yeah I get what you mean there.
Does not appear to be. It will be the first time ever that there is no trio.
That would be a first in Pokemon history, alongside the rumor that Kalos could now take Johto's title as the region to introduce the least number of new Pokemon.