If they animate Skull Kid like they would a normal fighter, it'd be weird, and otherwise he's about the same size as Young Link. I'm not saying it can't be done, but we have no precedent for a small, annoying-to-hit boss.
I mean, at least he'd be better than just a trophy, but I'd rather he be possible for DLC :S
Well, we had small bosses in the past, so I don't think it's totally out of the question.
Such as Metal Mario and some of the "shadow" (or whatever they're called) incarnations of characters in SSE.
While outside of the former, they weren't specifically designed bosses, but they still count.
So I don't think it's out of the realm of possibility if he just ends up as a stage boss, especially if he gets thrown off the mask eventually and you fight Majora's Wrath.
With that said though, I would love to see him as a character for the base roster or DLC.
I just personally wouldn't be surprised if he turns out to be an actual boss.