My guesses as to Mewtwo's palletes:
1. Purple, the base Mewtwo
2. Blue, a possibly unintentional reference to the first Pokemon movie in which Mewtwo had a skin tone that was much bluer than other designs, and a hold-over from melee that is used for team battles
3. Green, a light shade of green that references Mewtwo's shiny palette in the Pokemon games, and a hold-over from Melee that is used for team battles
4. Red, used for team battles
5. Pink, Mewtwo is uniformly a light pink, with little difference between his skin and his tail, a reference to Mewtwo's adorable progenitor Mew
6. Dark Purple, an inverted palette in which Mewtwo's skin is a dark purple and his tail is light gray, a reference to the Shadow Pokemon found in Pokemon Colosseum and Shadow Lugia's color scheme in particular
7. Dark Red, a palette in which Mewtwo's chestplate is off-black, with the rest of his skin being dark gray and his tail being a dark red, serving as a reference to Zoroark's color scheme
8. Dark Blue, Mewtwo's skin is a deep blue and his tail is a hot pink, with a tan trim for his chestplate, fingers, secondary neck, and sides of his horns, serving as a none-too-subtle reference to the Greninja-Mewtwo confusion that happened in the split seconds before Graninja's official reveal