Now, I know many of you on my f-list don't like this 'new' Pokemon, but please bear with me. I'd like to express my opinion and theories on it.
Now, obviously, we don't really know its connection to Mewtwo right now because Pokemon Smash! didn't reveal much. But they did reveal its classification: Genetic Pokemon (or at least serebii had this up, I don't know if this was confirmed in the show). There is only one Pokemon with that species name and that is Mewtwo. There are two ways to go about looking at that: one, it's a form of Mewtwo or two, it's a clone of a clone (ie. a clone of Mewtwo). Two is probably less likely because the movie itself is titled "Extremespeed Genesect: Mewtwo Awakens" and this leads us to conclude that Mewtwo will 'awaken' in some way and this is what I currently believe.
After I got over the initial shock, I began to really think about why they would decide to make a new form for Mewtwo, and why this form. First off, the title of the movie is a clue: Extremespeed Genesect. This tells me that one or all of the Genesects are extremely fast, maybe too fast for Mewtwo to handle during the movie, or else why bother putting it in the title? When I look at this new form, I see things designed for speed (think Deoxys speed form). Everything is streamlined and minimized. The loop on its head reminds me of a spoiler on a car which is used to decrease the amount of drag while going at high speeds. In other words, I think that this form is directly related to the speed of this Pokemon. The decision to move the tail to the back of the head is a bit more difficult to decipher, but if you continue to think in terms of speed and flight, everything is about how to reduce drag. The headtail creates a pathway for air to travel over the body that minimizes drag and thus achieves greater speed. It also gives the body a more teardrop shape which has been proven to cause the least amount of pressure drag in flight.
I don't think I need to get into weight or lift because, as a possible psychic Pokemon, it just levitates itself. But even with telekinetic abilities it still can't ignore air pressure during flight. It could just create a barrier, but that itself would cause a lot of drag.
The second part of my theory comes from how Mewtwo obtains this form. Many fans are speculating that Pokemon X and Y will deal with stuff relating to genetics because of the DNA symbols above the names. Obviously, we have little information to go on Pokemon-wise because they haven't shown us much (besides this little guy) so most will be just guesswork. But so far there are some theories; one, Mewtwo, like so many other Pokemon in the past, just naturally changes into this form with the addition of a specific item or move. Two, Mewtwo has been tinkered with by Team Plasma or Team Rocket (again). The first one seems the most likely since Mewtwo's backstory would make the second a bit farfetched.
So my theory is that Mewtwo will need more speed to beat Genesect and learning the move Extremespeed will trigger the form change. I could be wrong about this since the pre-order event Mewtwo's moveset doesn't include the move Extremespeed, but it does come holding the Custap berry which allows the Pokemon holding it to make the first move just once in a pinch. And Keldeo was first released without knowing Secret Sword so a second event Mewtwo isn't impossible (although in the game Keldeo can learn Secret Sword through a move tutor while Mewtwo can't learn Extremespeed at all).
And finally, my opinion on this little guy as a whole: I kinda like it now. The gameplay was what really sent it home for me, being all cute and floaty and sprite/pixie-like. I still don't like the design of its feet (they look like weird bird feets or something) but overall I'm okay with this. I may collect a few things of it here and there, but this guy probably won't be joining my collection full-time (unless something changes that sends me into a dangerous spiral of OMG MUST HAVE EVERYTHING).
I'm not really disappointed in this Pokemon, I'm way more disappointed in the lack of news. During DPP and BW we would get a ton of news when Pokemon Smash! aired or Coro Coro leaked. Now, Nintendo is keeping a tight lip about everything. We still don't know Xerneas, Yveltal, or Sylveon's types and they haven't even revealed a few of the common Pokemon encountered at the beginning of the game. So what's up, Nintendo? Why the hush hush about this game? GIVE US SOMETHING MORE, PLEASE.