I think they missed an opportunity with Team Flare. Mega-Evolution should have been discovered by the villains. Think about it. It would make them more powerful and threatening story-wise (and give you tougher fights), much like Cipher controlling Shadow Pokémon. It could also set up a "hunt down the Seven Sages" type quest from Black/White where you track down certain high ranking members and win a boss battle against their team, culminating with a Mega-Pokémon, to claim their Mega-Evolution stones. Right now, Team Flare seems fairly forgettable. Hopefully they'll improve as the story goes along.