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I have a theory about this.
So pretty much everything indicates that when they were making X and Y, for most of development they assumed they'd be making a Z or some other Kalos followup. They made ORAS instead and awkwardly dumped Mega Audino in there. I think it was planned for Z, where all the gym leaders would mega evolve and it would Valerie's ace.
Valerie's sleeves are Audino ears, which is extremely odd as it's pure Normal and she does not use one. I think they deliberately made Audino NOT Fairy Type as a reference to Valerie's planned story arc, similar to how the only reason G. Ponyta isn't part Fairy seems to be for story reasons with Bede. Valerie wants to be a Pokemon, but isn't one. So in the same way, they made her planned ace Audino seem to SCREAM Fairy Type but actually isn't one. And the mega evolution in Z was planned to coincide with a story arc for Valerie, either where she finally does become a Pokemon or where she accepts that she can/should not. So Audino becoming Fairy upon mega evolving would match up with Valerie's character growth where she accepts herself for who she really is.
