The greatest story of them all.
Theres a clear difference between a Pokémon being a generally good Pokémon overall in the metagame and people being forced to run it because they have such a narrow list of Pokémon they can run to not get totally rolled by Naga. Making that point also swerves the fact that both Heatran and Tyranitar are forced to run specific sets to actually be able to respond to Naga over the longer course of a game, SpDef Lefties and AV respectively. So what we have here is not only do you have to run 1 of about 3 Pokémon in order to be able to confidently defensively respond to Naga, you also have to run specific sets on them in order to do so. If this isn’t having an undesirable effect on the metagame by constraining player options to an unhealthy degree then I’m not really sure what is.