Have you ever played Pokemon like it's "meant" to be played?

Prove it.
"Because the manga says so" doesn't work as proof or make it true when it contradicts with half the original source material, i.e. one of the 2 pokemon games of that gen.

If we were going to take the official mangas as the canon, some of the key points to the ending to zelda: majoras mask is changed. BUT THATS OK, IT'S OFFICIAL! Sure, murdering the 4 kids wearing masks before fighting majora might be a LITTLE different to playing with them and giving them masks, then threatening the mask salesman, and destroying majoras mask instead of letting him leave with it, on good terms, but hey.

I answer your quote with something he posted earlier.

By the way, the creator of pokemon, Satoshi Tajiri, stated in an interview that he prefers the manga adaptation of pokemon than the anime. His envisioned world of pokemon more closely compares with the manga version, which is entirely different than the anime series and actually follows the storyline of the games more closely.