Don't see why people can't play a new pokemon game like a new game and leave their nostalgia at the doorstep.
I don't necessarily have a problem with them doing it since it's their game and I have no right to tell them what they should and shouldn't like. I only get irritated when people make claims about how they aren't really Pokemon, or moan about how awful they are without giving substantial back-up. I also hate that a lot of people seem to think that Gen 1 is somehow exempt from criticism.
Not to say that anyone on here is doing that, I want to be clear that most of the Gen 5 critics on here have been respectful about their preferences. I don't want it to make it sound like I'm yelling at anyone, because it's totally cool that you like earlier gens. Just don't use all your energy focusing on the negatives of the new generations, because a lot of people like and enjoy them.
I also think there are several reasons why they gave Mewtwo a new form. Namely, because it's themes have the potential to have cross-generational references. Not only does it fit in with Gen 5's Genesect, and add relevance to the movie, but it also fits in with the DNA theme that I'm assuming Gen 6 will include. That way, it can stay relevant throughout the generations and allow a connection to the past.
Also, what was the biggest criticism with Gen 5? The Pokemon. A lot of people didn't like that Gen 5 only had new Pokemon and didn't include the old ones.(until B/W 2). But it was still about 50/50 in who liked the new Pokemon and didn't. Mewtwo is a very popular Pokemon, and has always had the potential to have additions to it because of it's theme of gene manipulation. So as a throwback to older fans, they decided to add something that both old and new fans can play with. Mewthree has also been something that has been talked about since Gen 1, so this is probably a throwback to that as well.