I just remember something, and I think it'll be something nice to think about.
In Pokemon Colosseum, the main bad guys were Team Snagem, as they were on the news alot. BUT! They were actually a sub-group for the real villians, Team Cipher. Snagem supplied Cipher with Pokemon that were snaged, and Cipher turned the Pokemon into fighting machines.
Now WHAT IF, Team Flare is like Snagem, in the theory that that either they are a sub group supplying money for a bigger group for some big thing, or there are two divisions of Team Flare: One division is for the money grabbing, while the other group is focused on something else MUCH more sinister?
This is just an idea, so hopefully it isn't bashed against me too much ^_^