Hey guys. I am going to post something I wrote in the previous discussion area.
It would be really awesome, in my opinion, to only allow one megastone per party. Like in a battle, you can only have one of your pokemon evolve into a mega. This adds depth to the gameplay as you won't know which Pokémon has the megastone.
Maybe they will have a quest line for getting each individual Pokemon their Mega-item. Torchic comes with the Blazikenite/Blaziken Knight, but perhaps you have to talk to this new character, Koruni, to find out how to obtain the specific Mega item for each Pokemon. Also, they could involve the whole bonding-with-your-Pokemon mechanic. Maybe the Pokemon who likes you the most is the only one who can use the Mega item. I am not sure, but I believe GF would put limitations on how many/which Pokemon can use the Mega items and become a Mega-lution.
And actually, the more I think about it, the more I think you are correct (in response to Frezgle's comment). I mean, wasn't this new Mewtwo form created in a laboratory as well? Perhaps these alterations are from Team Flare experimenting on making super Pokémon. Black and White introduced the whole Black/White Kyurem thing with that item (forgot its name). It would not be a an off-assumption that this game would deal with alterations as well. For instance, we were talking about that DNA logo being present in the Japanese logo for the game, maybe this is what its all about?
Mega evolutions could be genetic alterations that allow Pokémon to reach their full potential. Perhaps there are two ways of going about it. Team Flare wants to make bank and sell these super Pokémon, and this reminds me of Gold and Silver with the Red Gyarados thing, where they tried to hasten their evolutions. Well Flare may have found a faster, yet terrible way to access Pokémon potential and want to profit off of that, but are terrorizing Pokémon through experimentation, while Koruni shows you how to bond with your Pokémon so they can reach their true potential in a good way.
This could correlate to the ethics of modification and be central to the story line. What is the ethical way to develop, and why is it wrong to force something to change? Perhaps this is why Team Flare is bad. It reminds me of the first two generations of Pokémon because of their motive for money, but a little more serious because they could be modifying and torturing Pokémon to gain that money.