Or Nanu has trained so well that he sent it in an undercover mission. Of course, all this might actually mean nothing at the end and they put a random intelligent A. Meowth in the episode just for the lolz and to showcase the species.
You mean, Nanu send it on an undercover mission so that gather info/uncover secrets about the villanious organization that is Team Rocket? Not a bad idea, but sounds a bit of a stretch unless they are bringing back Giovanni into SM for a villainous arc, a.k.a. Team Rainbow Rocket.