Alright, let's get a real debate in here. No Genwunner trolls and the like. This is a simple debate over who would win in a fight.

RULES:

Each Pokémon has access to all powers it can learn, and all powers used in the anime/movies, they are not limited on their moveset and may use them as they wish. As such, it also has feats of strength and feats of failure from the anime and movies to take into consideration.

Mewtwo does not have access to his Mega form for this debate because we do not know the details of what that form does and if it has any limitations. Additionally, this is to continue under the assumption that the Mewtwo depicted with the Mega form is a different mewtwo and are not to be taken into consideration.

Mewtwo
>Very intelligent, overpowered an Alakazam's mind with his own, and even rebuilt the cloning laboratory in a few months, perfected the cloning process that took years to develop, and had a plan to rule the world.
>Immense psychic power.
>Can psychically suppress all of the powers of at least 96 different pokémon (might have missed a few), and still hold his own against an ancient legendary.
>Has access to that ability that let him block and redirect a fully charged hyperbeam.
>Teleported an entire region.
>Has training from a master-level gym leader.
>Required several billions of dollars of weaponizing technology by the man that knew him and his weaknesses best, who happens to be a master-level gym leader, and even so had to willingly submit after being blackmailed to be defeated.

>Overconfident
>Cannot use his Dark Masterballs in this fight.
>Cannot mind-rape Arceus, even if Arceus does not have his Psychic Immunity active. No auto-wins.
>Cannot block Arceus's powers, even without Psychic Immunity active. No auto-wins.
>Cannot use that time-travel bullshit he used in the end of the first movie.

Cont, Arceus next.