There are so many conspiracy theories you could form around this game, I swear...
What Team Meteor is doing is actually for the greater good, in a way. The reason they're the evil party is because of how they go about it entirely- not caring whether you kill people to get what you want is despicable. I can understand the need to "fix" the City, as it has become a pretty crappy place (understatement of the century, that), but poisoning the lake and causing insane amounts of plant growth is a bit much.
I don't believe that Radomus is to be entirely trusted, that aside. He's even made a point with his whole "not everything is black and white" speech to make himself look suspicious. He's also an odd sort- the way he acts makes it seem like he knows more than he's letting on. Especially considering his reaction to the Amethyst Pendant being mentioned (and he later mentions, if you sided with El, that it's very important to him- but why?) and the fact that I'm 99% sure he could have brainwashed Luna, if he really wanted to. I don't think that he actually did, but that's beside the point.
And I guess I'm the only one who feels bad for Bennett? He does seem to want what's best for Luna but he's going about it in entirely the wrong way. He's doing that, though, because he trusts El on his word- he believes that she has been brainwashed. Something tells me that he would've just let her be were it not for pursuing that position in the Elite Four.
Never ask me to try and collect my thoughts or you get a jumble like this... Oh, lordy....