That seems interesting, but it also seems like a pretty huge shift in alignment from their current spot at "We wanna' take pokemon from kids for money." I'm not saying it couldn't happen, but I feel like there'd need to be a pretty good reason for it.
What might make more sense, is that Team Quantum forms after a brutal regime rises to power, and then people from all walks of life come to join under a single, rebellious banner. You could have gym leaders, Elite Four members past and future, Ace Trainers, and members from Teams Rocket, Magma, Aqua, Galactic, Plasma, and Flare coming together to oppose a threat greater than any of them, only to be pushed back to their furthest bastions, and eventually deciding to stake everything on a risky gamble of traveling back into the past to stop whatever evil takes control before it even begins. In order to insure that the horrors of their timeline never come to pass, Team Quantum decides to start an empire of their own, planning to eventually bring about massive scientific and social advancement, but forced to make some moral sacrifices for what they see as the greater good.
This way, they've got an understandable goal, reasonable ideals, and intensely evil methods, making them (in my opinion, anyway) the best kind of villains.
Plus, as another bonus, you can have all sorts of memorable characters show up. Maybe they're financed by Giovanni and Lysandre, where the time machine is designed by Cyrus, and groups of scientists from all the teams. You could have Maxie serve as a strategist, hungry for revenge against whatever force took his beloved Team Magma away from him. Perhaps some teams have been crushed, or their leaders were killed. Heck, maybe Team Plasma sided with the regime...
There are a lot of options.
Oh, also, there was some talk about getting legendaries, towns, and maybe a map commissioned. There's someone by the username of "Desu Juice" who's doing some pretty rad art commissions for pretty cheap. It's good art too. I was actually thinking about getting them to make some art for a few characters of mine, and I normally don't get commissions.
