I think it might be coincidental, though I did think initially that Wii Fit Trainer having the Deep Breathing technique did hurt Shulk's chances for inclusion; even the Wii Fit Trainer's inclusion alone did that in a way (as Wii Fit Trainer is a character who represents a Wii debuting series, much like Shulk would as a Xenoblade Chronicles representative).
I haven't played Xenoblade Chronicles so my understanding of things Shulk can do might be limited, but as far as my research goes, the only particularly unique thing I could thing of for Shulk move-set/mechanic wise is having a self-buffing move much like Wii Fit Trainer's Deep Breathing. I'd say it will have had a minor impact on Shulk's chances, though I wouldn't pin down Wii Fit Trainer or the Deep Breathing technique as the sole reason if Shulk ultimately does not get in as a playable character.