I guess I've been playing RPGs long enough to the point where you notice the game isn't that subtle on revealing who the villains are.
When starting the game, you get news of Team Flare, and encounter an NPC with bright tall/spiky red hair... It's one of those sarcastic moments of 'Gee, I wonder who this guy in red hair really is' while in a bright red cafe... To be honest, Team personality is a bit weird, but I'm also not a fan of the bright red.
Storywise, I guess it is a bit interesting, especially on the background and history of it. The game talked about a 3000 year war, with a weapon that resulted in the death of many pokemon and humans. Apparently, that's how it influenced Lysandra. Had some 'selfish' goals, and was also afraid that the population would overgrow too much to sustain itself.
It's a weird plot, but oh well. It felt a bit more morbid and mature than the previous games, that's for sure.