It's only anecdotal, but I'm fairly certain Nattorei is the most used Pokemon, and among highly rated players at least its usage seems to be in the neighborhood of 40% or so, if not more. Nattorei has the unique attribute of being a Kingdra counter (aside from Empo lol), does fairly well against a lot of other rain Pokemon, and incidentally is also a good check for Latios.
I don't know about the rest of you, but when I slap Natty on the team, the thinking is usually that I need a Kingdra counter, I need to be more solid against Latios, so I need Nattorei. The abundantly high usage of Nattorei and the lack of other good options to check either Latios or Kingdra (Latios has a few, but Natty is among the best of them) suggested to me that there was a problem with Kingdra and Latios.