That's got me thinking... how would Sonic and Mewtwo interact?
Assuming post M1 Mewtwo (After it learns "what you do with the gift of life", etc), then it'd likely be more accepting and intrigued of Sonic.
If Pre M1 Mewtwo(PSYCHIC STORMS AND CLONE WARS M8), it'll probably be annoyed to oblivion.
M16 Mewtwo doesn't seem to mind anyone on the good side.
OriginsTwo will likely be the most savage. Intellectual, yes, but probably the most cold-hearted (at least initially) towards Sonic.
Sonic probably wouldn't mind Post M1 Mewtwo as much due to it being less villainous and more of a neutral or anti-hero-ish character, and would probably interact with it, at the worst, in a similar fashion as he already does with Shadow. Sonic's pretty open when it comes to interacting with those who aren't on the bad guys' side.
If Sonic/Pre M1 Mewtwo, Sonic will likely try to stop Mewtwo and not befriend it until after it learns the error of its ways.
If Sonic/M16 Mewtwo, they'll be fine.
If Sonic/OriginsTwo, Sonic would probably be more snarky with Mewtwo as to noticing its hostile nature, but not noticing any real villainous motives (such as how Pre M1 Mewtwo was). They'd probably end up fighting in Cerulean Cave or something.