At first I was going to argue that while they think they're doing good, they're also causing a lot of problems for other people in the process, but I actually see what you're trying to say. Why would a team that thinks it's doing good only use Pokemon that are supposed to be 'evil'?
Well there are a lot of new Pokemon out there now, and so I'd have not objections if the Hoenn Dex was expanded a bit. There just aren't a whole lot of fire alternatives for Magma. Maybe they could use ground or rock types?
I also would love to see them (or any team for that matter) have more involvement in the storyline, or at least more well tied together involvement.