a Legendary is not simply an individual Pokémon about which legends are written, but differs from regular Pokémon in key ways.
Put another way, what makes Mewtwo legendary ISN'T the fact that there's a legend behind him (because there isn't, at least not directly), but rather the fact that it's different from regular pokemon in several key ways: only one per game, exceptionally powerful, extremely difficult to capture, unable to reproduce through breeding (as I said above), and not part of an evolutionary chain.
All those traits make it legendary by definition of the industry term (a.k.a. "term of art") "legendary."
The above post was typed in front of a live studio audience.
Ya know, if you really think about it, doesn't the fact that nobody talks or knows about mewtwo make him even more legendary than most? Think about it. A lot of people in the pokemon world know about Arceus and the trio and what not...but then there's the legend of how Cinibar islands laboratory blew up, the remnants of papers scattered about with the description of a pokemon made from mew, and then the sightings of an incredibly powerful and unknown pokemon who lives deep within the scary ass cave near cerulean city. To me, that sounds more legendary than most. There's definitely a legend about mewtwo, it's just that not every body has heard the legend. I'm sure there's people in the pokemon world who hasn't heard of the three musketeers or arceus, but it doesn't make them any less of a legend.
Thats what im thinking, about Cinnbar Island
They dont know of Mewtwo, but they know of something...
Think of the other legendaries as being like dragons and chimeras in our own world, and Mewtwo as being a scary urban legend
"Er kann mich am Arsche lecken!"-Goetz von Berlichingen [Papal Crusaders]