I know the Japanese version casts Mewtwo in a much better light, but what sort of differences do both plots have?
Doing some research on the plot summary in Bulbapedia, the only key difference is the opening sequence, showing Mewtwo's interactions with Giovanni. From what I recall, these were actually addressed in the anime only (if it even aired) in America.
The other difference I found, though this may just attribute to my memory being fuzzy from not seeing it in a while, is that the American version does not have the tale of the Pokemon resurrecting humans with their tears, making the ending scene with Ash a lot more...mysterious.
I just saw the Japanese version, and it is very different! The biggest difference is that, at the beginning, there is the story of how Mewtwo grows up. This way you have an understanding of how he reacts this way.
Later on, many conversations between people are different, and you get the story in a different way. When I say many, I mean 80% of them.
I found it on YouTube with English subtitles. Try to watch it and you will understand what I mean.