Team Flare's boss is Blaine - the Cinnabar Island (Fire-Type) Gym Leader. While he was a gym leader, he sent thieves into the mansion on Cinnabar to recover the research notes pertaining to the Mewtwo experiment. This is why you find the key to the gym inside the mansion, and thieves in the mansion as well as in his gym.
Years have passed, and he has turned his thieving lackeys into Team Flare. The lackey's are only in it for the money (being thieves and all), but Blaine has been trying to use the data from the Mewtwo experiment to create an even more powerful Pokemon (hence, the new Mewtwo forme(s)).
What do you think?
1: If you think your opinion is fact, then I will ignore you. 2: If you butcher the English language or abuse Netspeak, see #1.
Your theory is brilliant, I had a similar idea when I first heard the team will be called team flare. I put the pieces together like you did and figured that there was a connection with the new mewtwo form. I hope it actually plays into the storyline though.