Let say Mewtwo was given moody
Completely irrelevant. Mewtwo doesn't have Moody, and won't have in this generation. Besides, Moody is a special case (see: banned in Ubers), so using it doesn't help your case.
Uber pokemon are irrelevant in the standard metagame, and thus should not be given any consideration in such bans. Without Lugia you have only Dragonite, one pokemon, 2 abilities.
Lugia and Dragonite are OU. Lugia is found to be broken, Dragonite too. People ban Multiscale because it's the common factor. Lugia is still broken, Dragonite isn't anymore. Lugia is then banned, Dragonite now sucks. What has just happened here? A pokémon was nerfed because we didn't want to ban it, and we ended up with two bans anyway; one of them, however, was completely against principle (and
common sense), because we wanted to work with this asinine logic of "well the pokémon,
the main element in competitive pokémon and what's always banned at first, shouldn't be banned if we could nerf it instead so ban Multiscale yeahhhhhh".
BTW: I don't think Dragonite should be banned either way.
Neither do I but eh, I'd rather see Dragonite banned than "Multiscale". Multiscale doesn't even work like Drizzle to have a vessel argument in its defense...