In my opinion, everything is canon, just in separate worlds. As it's pretty obvious that Pokemon has several multiverses and different timelines where similar events occur, but fold out differently. Think of it like every single Pokemon cartridge is a different "world" but the story folds out the same, and the legendary that appears depends on which version of the "world" you're in. (Since you can never meet Palkia in the Diamond "world", for example.
Anyway, the anime and manga are completely different takes on the franchise and really shouldn't be compared. And, the Gym Leaders in the manga were only evil in the first manga chapter. Not only were they not evil in the R/S chapter, they weren't in the D/P chapters and so on, either. In fact, I'd say they were pretty similar to their game counterparts after the R/S saga.
In the anime, unless the Gym leaders travel with Ash, they're barely focused on and thus don't really appear after Ash beats them. Like, most of the Kanto leaders only appeared once with some very few exceptions in Surge and Erika, I think. And this honestly followed suit in every single series up until I guess Journeys where some got a reappearance.
But, really, it's not fair to compare the "canons" as they are wildly different. I've read up until Sun/Moon and haven't finished that one, but the stories are all meant to be seen as their own thing.
Also, I just want to say counterparts =/= the same character. Lady Berlitz is not Dawn. Sapphire isn't May, etcetera. They are completely different characters that shouldn't be treated as the same ones.