I think Team Flare will be one of those organizations who says that they have a goal which may seem beneficial, but either there's some sort of plot twist and it's much more than that, or they are extremists, sort of like Team Magma and Aqua(who were laughably the worst in terms of goals, no debate necessary).
I also have a feeling that they will appear as a villainous team to the protagonists, but to everyone else be the good guys. Kind of like manipulation, except not the stupid kind of manipulation like in Black and White. This would really add to the theory of being an underground, two-faced organization.
It would also be interesting to say that they invented Mega rings, and sold them to popular trainers like gym leader Korrina, and that actress lady Diantha. Some DNA splicing wouldn't hurt to be included in to their schemes, after all they have scientists. But then again, where would we get ours from?