You should also probably have your entire plan come down to a single pokemon battle. Get some kid to confront you moments before everything goes perfectly, and have him challenge you. Then, make sure you inexplicably respect a defeat in said battle as a defeat of everything you stand for and as a reason to give up your life of crime. Don’t worry. That probably won’t happen.
Specifically for team flare though, where did that guy find so many pokemon trainers that wanted to kill all the pokemon? I can buy that Lysandre himself was crazy enough to come up with the plan, but that’s a lot of people who have spent their lives raising pokemon and all want to wipe all of them out of existence. Those two things seem pretty mutually exclusive.