I mean Vaati is literally the most reccuring antagonist beside Ganon in the canon games while Skull Kid is not even the antagonist of his own game. If another Zelda villain would get in Smash Vaati makes more sense.

Also he was snobbed from HW for some reason despite being probably the only missing character to make this game's roster pretty much perfect when it comes to representation.

A lot of people I know requested Vaati back during Brawl, and were pretty bummed out he didn't make it in Hyrule Warriors. :(