Well, I don’t really know the manga, although I am aware that it’s a great deal darker than the anime or games. Also I think (?) it’s not actually produced by Nintendo or Game Freak, but sort of authorised by them in some vague and nebulous sense? I admit I don’t really know what the situation is there.
(I wish to point out, because I know someone will bring it up, that when Satoshi Tajiri said of Pokémon Adventures that it “most resembles the world [he] was trying to convey” he was comparing it to other Pokémon manga series, not to the games or anime- that quote has an annoying tendency to get taken out of context)
As for the games and anime… well, to be honest, I don’t know that I see the point in choosing. They just don’t do the same things. I mean, they notionally portray the same world, and I tend to think they’re fairly consistent with each other in their outlook and broad conceptions of what makes the setting work (i.e. ”the power of friendship”), but the purpose of the anime is to tell a story, while the purpose of the games is ultimately to provide challenges in strategy and problem-solving, with the story very much being a secondary concern (sure, the storytelling has been improving a lot recently, but you don’t have to look far to find video games that make it seem downright primitive). You can’t play the anime, and the games can’t tell as good a story or contribute as much to our image of the background world (although again that’s changing). For me they’re two parts of a larger whole.
Pokémaniacal 