It's like no one realizes that there are levels of canon. There is no ONE CANON. In fiction, there are often contradictions, where it becomes necessary to separate which souce might be more canon than another.
For instance: The Halo books. They are canon, but the games take precedence if the two disagree. The only thing higher than the games, in my opinion, is a statement from the creator, commonly known as Word of God. As an example, Yoshio Sakamo has stated that Samus' suit takes a constant amount of concentration impossible for a normal human. There's no evidence of this in the games, but he's the creator, so his word goes.
Pokemon has something similar. Creator > Games > Manga > Anime > Other stuff, like the card game. The anime can be used, but only if the games don't disagree. It's useful for things the games don't show, but nothing more.
I think stat distribution is a gameplay mechanic specifically in place to keep the games balanced. Sure there is a correlation to a Pokemon's actual abilities, but not always.
In the games, it is pretty much impossible to beat an Aggron with a Jigglypuff, but in the anime and manga, it is very possible. There are lots of other examples, too. Due to the game stat distribution its impossible for something like Mamoswine to do better with Special Attacks than Physical, but in the anime Dawn's Mamoswine actually did more damage to something with a Hidden Power than a Take Down.