Pokemon is a strange case. In Brawl, the Pokemon spinoffs are more or less completely ignored, only the anime is used for the voices and the console titles are used for the 3D Pokeball Pokemon models. All of the music is from the mainline, and there are no trophies or stickers referencing the spinoffs; in fact, every single Pokemon sticker is actually just official Brawl artwork of the Pokemon that appear in it (completely diametrically opposed to the anything and everything of the other series).
Melee had a single trophy from Pokemon Snap, and that was about it.
The Pokemon Company must have fairly strict stipulations about the series, moreso than Nintendo has on the other series (Sakurai did state as much before). Though I'm still not sure how Jigglypuff fits into all that, because it still remaining in the roster strikes me as a Sakurai decision, so he must have some clout on what goes in when it comes to Pokemon.
That's my little tangent on the subject.