If you want to blame the lack of Zelda playable characters on anything, I think the structure of the Zelda series itself is at fault here. The whole series is about the Triforce and its three holders: Link, Zelda, Ganon. Almost every other character is fleeting, making one-off appearances (Tingle and Impa notwithstanding). Are characters like that "worth" of being in Smash Bros.? Even within the same series, what makes Skull Kid more "deserving" (I also hate this term, but let's roll with it) than Vaati? Ghirahim? Hilda? Zant? Or helpers like Midna, Fi, the BOTW Champions?
Don't get me wrong, I've got nothing against Skull Kid. But I do think most people are overestimating his chances just because the Assist Trophy went MIA. In my opinion, Zelda doesn't need more characters. Having a bunch of Links is actually a good representation of the series lore, being that "Link" is never the same character. It's a series that thrives on its main trio, and everything else (hi Sheik) is just a bonus.