This is gonna sound crazy, but I feel like there might not be an evil team. I think the bad guy in this game is Kyurem, and these lovely red-haired people right here are just an environmental organization created to fix the sudden freeze caused by one (two?) dragon(s). Just guessing but it sounds believable to me.
And why is professor suddenly evil? I know he has a "I'm a nice guy with hidden intentions" feel to him, but maybe GameFreak expected everyone to immediately peg him as a bad guy. I for one think he's a nice person with no global domination schemes up his sleeves.