It is still canon, just not in game verse. Just because something different is in the anime doesn't make it less qualified for what is canon in the Pokemon world. The games, anime, and mangas have different interpretations of the Pokemon world and each one can be canon. It just depends which verse you'll go with when you do fanfiction.
EDIT: On the other hand, there is mention of the Ever Grande conference, so I guess it's animeverse! @_@ I'm just confusing myself now.