They wanted to create the perfect being and they succeeded... quite, they somehow forgot to feed him well or put something inside him other than air.
I mean the thing is barely heavier than jigglypuff! A FREAKING BALLON!. This only applies to smash because in the games he weights something around 260 lbs.
They really thought it would be a great idea to make pikachu weight look like snorlax when compared to mewtwo. Oh an the trophy explanation is just the icing, it says something along the lines of using his psychic powers to make himself lighter, because of course the most intelligent entity in the game would think that dying earlier is the best strategy. Now weighing the same as a pencil makes you less prone to combos... when you are tiny of course, mewtwo is not.
Maybe his weigh will get patched eventually so this comic will make no sense for the future generations, so just a note for people of the future : As of patch 1.0.9 the ultimate being, the psychic ultra powerful mewtwo was lighter than a mouse, a 2-D drawing, a kirby, a dog, an astronaut not bigger than an inch and mother cosmos just to put it into perspective.