Mewtwo's mobility is much better than Ganondorf's allowing Mewtwo to run away and charge shadow ball easily, which forces Ganon to approach Mewtwo and Ganon being slow shadow ball can zone him easily. With many of Mewtwo's moves being safe its hard for Ganondorf to punish and edge guarding is in Mewtwo's favor. Mewtwo is light and Ganondorf has powerful moves ,Mewtwo's tail hurtbox is larger than in Smash 4 ,air dodging nerfed and Ganondorf having sword smash attacks which all hurt Mewtwo, however ganoncide was nerfed, Ganon's up smash is more punishable and bair hitbox is smaller than in smash 4 which help Mewtwo against Ganondorf.
Mewtwo wins this MU.
Mewtwo's mobility is much better than Ganondorf's allowing Mewtwo to run away and charge shadow ball easily, which forces Ganon to approach Mewtwo and Ganon being slow shadow ball can zone him easily. With many of Mewtwo's moves being safe its hard for Ganondorf to punish and edge guarding is in Mewtwo's favor. Mewtwo is light and Ganondorf has powerful moves ,Mewtwo's tail hurtbox is larger than in Smash 4 ,air dodging nerfed and Ganondorf having sword smash attacks which all hurt Mewtwo, however ganoncide was nerfed, Ganon's up smash is more punishable and bair hitbox is smaller than in smash 4 which help Mewtwo against Ganondorf.
My vote - Ganondorf 4 / Mewtwo 6