As for Magma, I think it was the writers' favorism: immediate appearance in AG 2, success in Slateport, plus the Mt. Chimmey plot turned out to be theirs, the last minute surprise of Bannai and Maxie's well-written character and viewpoints (vs. Archie's stereotypical villain one). Sad to say, the writers still dropped the ball, but it was clear that the writers were more pro-Magma as the arc turned out.
Anyway, first intro-wise, Aqua. Good subterfuge into Devon and an actual episode dedicated to the agent's escape. We never get that, normally. Plus, Shelly/Izumi was awesome as a drama queen, and that shouldn't be ignored.