For Mewtwo, the basis was Mew. For Shadow, the basis was not, actually, Sonic — at least not in universe. The legendary ...

Z-A remains unknown: the legendary Groudon, Kyogre, and Rayquaza. When Mega Evolution was first introduced in 2013, only one legendary Pokemon was able to Mega Evolve: Mewtwo into Mega Mewtwo X and Y.