I actually like Team Flare a lot. Their outfits are very out there.
While their goal to make money is simple, this may actually make them even more destructive than usual.
See when people are greedy, they will stop at nothing to acquire what they want. Since Team Flare is just interested in making a profit, I can see them doing whatever they can regardless of the consequences. I wouldn't be surprised if their actions drastically alter the environment and Pokemon as an unintended consequence. Maybe someone will pay them a large sum of money to capture Xerneas/Yveltal and when they do capture them everything goes awry.
I actually like that Team Flare seems to be legitimately evil. While it's nice to see stories with evil teams who are seriously misguided in their attempts to make a better world, someone who just doesn't care and will do anything and everything will definitely be fun to take down.