Rayquaza takes it with 21 different set-based cards. If full arts, reprints, and alternate artworks are considered, Rayquaza comes in at 29.
Charizard has 19 different set-based cards. However when the full arts, reprints, and alternate artworks, and things like _____ Charizard are considered, it comes in at 28.
Keep in mind that none of these include promos, reverses, or jumbo box toppers.
I know I have seen concept art for the original pokemon games and I am trying to think of the first few pokemon they created but I can’t remember where I was reading about that. As far as TCG goes my guess would be on the trainer decks as being the first thing sent over here, but I am not sure by any means.