I was hoping SO BADLY for Sycamore to be revealed as the leader of Team Flare, because that would have given the story an actual twist and made it so interesting, but alas...
I don't dislike Team Flare. Dare I say, they're at least better than Team Rocket, in that their goals stem beyond just making money.
Lysandre is one of the few real "characters" in XY, and while he could have been presented better he does have a certain tragicness to him that makes him one of the more interesting villains in the Pokémon games.
Lysandre wants to "start the world over with only the good people," but to "be a good person" means joining Team Flare and that means having to pay a ton of money and nothing more...obviously he can't think this is what defines a good person, right? Honestly, it's all about the little details with Lysandre, and seeing as how he needed lots of money to get his giant death machine up and running I wouldn't be surprised if he wouldn't even let the rest of Team Flare survive--or even himself. That's tragic.
He admits that he knows what he's doing is wrong, but he is extreme and has become obsessed, which makes him multifaceted and interesting (and tragic). I think the biggest flaw was making the Grunts so silly. Game Freak wanted them to be a sillier, wackier team, which the Grunts pulled off quite well. But then having the leader want to commit mass genocide just...well that isn't silly at all. This juxtaposition makes for a very interesting thought, though: the Grunts really put a lot of faith in Lysandre, so much so that they didn't feel the need to take things seriously. They thought everything would work out in the end in their favor. This solidifies Lysandre as a man of great power and leadership--we know that he created the Holo Caster, but besides that we don't see a whole lot of his influence, so it's interesting to think that the Grunts, by being silly and outlandish, essentially confirm the kind of influence this man really has.
Another interesting thing on the topic of influence is Malva. We see her as the Holo Caster news reporter, and later as an Elite Four member. After the events at the PokéBall Factory, it seemed odd that Malva would report that they "have no information" on what happened...but when we later find out that Malva is a part of Team Flare, it becomes clear that Lysandre used his power and influence to corrupt the news, so Team Flare could go about their business with as little interference as possible. Talk about sinister!
So in the end, I think Team Flare's biggest downfall is that they have the opportunity to be one of the more sinister, destructive, and threatening teams, but the juxtaposition of silly Grunts with serious Admins and their leader just doesn't work the way it could have.
