Mega_Mewtwo is currently aliased to "Mega_Mewtwo_Y"
https://e621.net/wiki/show?title=mega_mewtwo_y

I suspect this alias was temporary so as to transfer all the "Mega_Mewtwo" tags to "Mega_Mewtwo_Y" once the character was verified as the Y-variant. (Akin to how "Mewthree" is aliased to "Mega_Mewtwo_Y" due to back when it was a nickname/placeholder until the actual name was revealed.)

Mega_Mewtwo_X is also a variant of Mega_Mewtwo.

Mega_Charizard_X and Mega_Charizard_Y both share the Mega_Charizard tag

The Mega Mewtwos cannot share the "Mega_Mewtwo" tag due to the alias, and it could cause Mega_Mewtwo_X to erroneously be tagged as Mega_Mewtwo_Y when also tagged as Mega_Mewtwo.

Additionally, just as Mega_Charizard_X and Mega_Charizard_Y are both implicated to Mega_Charizard, Mega_Mewtwo_X and Mega_Mewtwo_Y should be implicated to Mega_Mewtwo as well.

Proposal:
Remove alias Mega_Mewtwo → Mega_Mewtwo_Y
Add implication Mega_Mewtwo_Y → Mega_Mewtwo
Add implication Mega_Mewtwo_X → Mega_Mewtwo

_{That was a lot of Mega_X/Ys.}

Highly confused reading this, but fortunately I already know what you meant already so fortunately I don't have to parse it all. :V

I've made the following changes:

Alias: mega_mewtwo -> mega_mewtwo_y (deleted)
Alias: mewthree -> mega_mewtwo_y (approved)
Alias: mewthree -> mega_mewtwo (approved)
Implications: mega_mewtwo_y, mega_mewtwo_x -> mega_evolution, mewtwo (deleted)
Implication: mega_mewtwo -> mega_evolution (approved)
Implication: mega_mewtwo_x -> mega_mewtwo (approved)
Implication: mega_mewtwo_y -> mega_mewtwo (approved)

I left off the mewtwo implication since all mega_[pokémon] -> [pokémon] implications are likely be deleted soon anyways (it just hasn't been done yet).