My Illogical Theory
My illogical thought is that maybe they thought Mewtwo wasn't very 'legendary'.
Mewtwo was one of the first legendaries in the Pokemon series. There was Zapdos, Moltres, Articuno, and then there was Mewtwo. Everyone knows Zapdos, Moltres and Articuno as the 'legendary bird trio', but who remembers Mewtwo? It wasn't part of anything special - it was just sitting there in Cerulean Cave waiting to defeat someone yet utterly fail in being enclosed in a PokeBall and possibly a PC for the rest of it's useless life.
The Legendary Bird Trio was actually part of the storyline of Kanto games (i.e., not Gen II and Gen IV remakes). Mewtwo was just an option as a challenge for whoever wanted to go through Cerulean Cave and get this awesomely yet mutated Pokemon. It was never really known.
Also, Mewtwo is commonly associated with what you would think as the puny Pokemon Mew. No, it's not puny, however it looks puny. Since these two Pokemon are commonly associated, with Mewtwo being a redo of the Pokemon, it's not thought of that often, it might actually be put down due to this connection.
Due to it's unpopularity, they probably wanted to bring the awesomeness of original Mewtwo in another form. (They could obviously just put him/her in the damn storyline, but Game Freak ain't that logical. Like my theory. x) ) Yes - the awesome new Mega Mewtwo! More powerful then your favoured Mewtwo! Stronger stats! Impress your friends with an even stronger Legendary!
Imagine that? That really awesome flyer that shows that (even though it's not a distribution, but imagine if it was) you have to get this awesome Mewtwo so you can beat all battles in your way!
I went a little off-topic there. Hm. xD
So - here, they bring back the spark of Mewtwo once again in an even greater form. Since it was the first Mega Evolution ever announced, Mewtwo might get back it's popularity once again! Of course, Game Freak is doing their best to bring back this really awesome title of being legendary.
They try to bring more legendaries every generation to make even more opportunities to own your friends. Since every one was complaining about it, they thought:
Awesome Person: Hey! I've got an idea! Instead of making the new legendary Pokemon Koh-Koh - you know, Ho-oh's twin brother - why don't we enhance the power of other classic legendaries?
And that was why the made it. :3
I think I supported this well, so Hope I helped. :)