(( Note: I'm not sure if this is where I should put this. ))
Shadow the Hedgehog and Mewtwo. They're pretty similar, I think. I'm going to try and point out, in as much of a non-crazy way I can, the ways that they're the same. (You can blame Saturday-morning SonicX episodes for this.)
First of all... Both Shadow and Mewtwo have a yasashi-girl character. (see http://www.geocities.com/soulofaitwo/miiai.html for meaning of 'yasashi-girl'.) Ai died, and Fuji's whole research was about cloning her, bringing her back to life. Maria Robotnik, Shadow's yasashi-girl, had a life-threatening disease that Gerald Robotnik was working to cure. Both Mewtwo and Shadow were experiments created not only to be powerful, ('The most powerful Pokémon in the world' and 'the ultimate life form'.) but also as part of an experiment to save the yasashi-girl. The yasashi and the experiment became best friends, but the yasashi died.
Both Mewtwo and Shadow have a general dislike of others, while both also have good qualities to them. Mewtwo at the end of his first movie, and Shadow in many different times in the series.
That's just what I think, at least. But really, how many people who like both characters wouldn't like to see one of Shadow's Chaos Controls go wrong and teleport him to the Pokémon world? ;)