That would mean they shouldn't include Eusine in HG/SS because Crystal's story is not canon. I don't believe they will ever don't count third game as canon.
Actually, third games are more important as canon because they contain more expanded storyline. In B/W Cynthia compares player to that trainer who encountered Giratina, referring to canon event she witnessed in Distortion World in Platinum. All third games are counted as canon.