Vaati's games were not very popular. Legend of Zelda 4 Swords Adventures is the worse selling game of the Zelda series.
Like Swampasaur said, sales don't matter to any great extent. Having a major appearance in multiple Zelda games is enough to elevate a character above one-timers (or characters with only one major appearance), as recurring major characters outside Link, Zelda, Ganondorf, Epona, Impa, and Tingle are few and far between. Again, I don't think Vaati has a good chance either, but Skull Kid is hardly more likely. In reality, neither really has much of a shot.
Skysword Sword was the worse selling of the major 3D Zelda console releases. It was behind Ocarina, Twilight, Majora, and Windwaker.
The second Zelda on a system always sells worse. However, SS did sell better than MM, maybe check your numbers again. But again, sales don't matter. If you don't think SS is going to get the majority of the Zelda content in SSB4, you're a bit naive.
Under the recent logic, I guess we should cut Ganondorf and Sheik as well since they haven't been recent. Also if you want to step outside of LoZ series, why not cut Marth from FE because he is no longer relevant. I don't really think it works that way.
Yeah, because a character with one major appearance is equal to that of the primary antagonist of the whole series. Also, adding a character who hasn't had a recent appearance is hardly the same thing as cutting an existing Smash character without a recent appearance. As for Marth, I guess recent remakes of two games, major referencing and highly-promoted DLC in Awakening, and SMTxFE don't count as relevant.
As for when he wasn't recent, like around Melee and Brawl, being the most popular character, having a major role more than once in a series with a changing cast, and being the most iconic and "face" of the series do count for something. Skull Kid can't claim to have any of these. He's hardly the most popular character in his series, he's only had one major appearance in a relatively static cast, and the only thing he could be described as iconic or the face of would be his one major game.
Tingle maybe a good point but his absence from major Zelda titles in recent history does speak volumes.
You do realize you're arguing for a character who has also been absent in the last three Zelda titles, and hasn't had an important role for the last ten?