to this mewtwo is based on giygas theory
Mew is said to be the ancestor of all pokemon (according to first gen.)
but there are some extraterrestrial pokemon like clefairy, mew is still the ancestor
also mew is able to fly through the vacuum of space (you can see this in the original Pokemon, and in pokemon snap, where you got an entire level for mew in space)
so according to this, mew could be an alien (well it's very likely)
so this would make mewtwo an alien like giygas (or at least a copy of an alien)
if you look back at the first generation of pokemon, there is the pokemon mansion on cinnabar island which has to do with mew and mewtwo
many people think mewtwo is just a clone of mew, but according to the scientific logs you can find there, mewtwo is a clone of the embryo of a pregnant mew ... hmm does this embryo-stuff sounds familiar?
in the pokemon movie, mewtwo is a clone of a fossil of a mew, but the movie came out after the game ... and also it's a movie for kids, they had to change this because you can see how they clone mewtwo at the beginning)
when mewtwo escaped and destroyed the lab where he got created, giovanny appears he can help him to control his powers, but the point here is he says they can be partners (so Giovanny and mewtwo)
later, after Giovanny tested the powers of mewtwo and helped him to control them, mewtwo asks what the meaning of his life is, and giovanny says mewtwo has been created to fight for him and he says they'll never be partner (like he said at the beginnig), giovanny will be the master
so mewtwo got betrayed by giovanny. then he escapes again. he got betrayed by humans
in mother 1, george studied the psi-abilities of the aliens without permission, so he betrayed the aliens and has stolen there secret powers. Like giovanny betrayed mewtwo to get his powers, george betrayed the aliens to get their powers
both (mewtwo and the aliens) hate the mankind
both powers are psycho-kinetic based, so you could say they're somehow the same (yeah, no pk-fire or pk-thunder etc. in pokemon, but you know what i mean)
mewtwo is the strongest pokemon known to mankind (1.gen)
and in mother these psi-powers are the strongest they've ever seen
yeah, all of this is just a theory
but many developers, who created the mother/earthbound series worked on pokemon later, and there are just so many similarities
so for me mewtwo is based on Giygas
... and just look at Giygas (mother1) and then at mewtwo
they just look like the same