I tend to think Skull Kid/Majora's Mask are the most worthy contender for Zelda representation for a number of reasons. First and foremost, Majora's iconic status and game's popularity, that's endured the test of time and has such a large fan following that it got a 3DS remake largely because there was so much demand for it. Secondly, however, I feel there's a Skull Kid shaped hole in Zelda's representation. From early Melee, Zelda's representation has been modeled after characters that each had a significant role in the journey of the Hero of Time - who, while not having been in a Smash Bros. game since Melee - is arguably the most well known and iconic iteration of Link (welcome back, Hero of Time!). Each of the most important figures in Link's journey made the transition: Zelda, the eponymous princess in distress who orchestrates Link's adventure. Sheik, Link's mysterious guide and mentor throughout the frightening landscapes and trials of future Hyrule (bearing a significant resemblance to Impa). Ganondorf, the King of Thieves - Link's immortal enemy. And Link's young self, before his outset into the future. Even Navi is represented in taunts.
Every stage of the Hero of Time's adventure is chronicled, from the naive Kokiri wannabe, to the adult that stepped out of the Temple of Time into ruined Hyrule, to the mentor that guided him throughout that perilous land - as well as adulthood - all the way up to the final conflict of the three Triforce wielders. Of course, Link's conflict didn't end there, as he still had one more adventure left in him, involving an old friend going back to his childhood roots in the Lost Woods, a parallel world, and a villain possibly as formidable as Ganon himself.
Heck, even Sakurai thought this chapter of Zelda important enough to cover by giving Majora’s Mask two stages in Melee (Great Bay, Trophy Tussle 3), barring representing Skull Kid himself as an actual character (who was thereafter one of the most requested characters even since Brawl days). Yet for now, this important chapter of the greatest Link’s adventure remains untapped.
To me, Skull Kid also represents a bit of everything that's been asked for in a Zelda rep. As an old friend of Link, and bearing the fairies Tatl and Tael, he has that friend/partner status you'd want in a rep like Midna, Tetra, or Fi. As a villain, he represents the series' most recognizable foe behind Ganondorf, and probably one of the most unique villains in gaming. He represents the whimsy and weirdness of Legend of Zelda in ways you'd likely only find as completely in a character like Tingle (or Groose), with one of the best character designs I've seen for a gaming icon. He has the tragic fall from grace and sympathetic backstory of characters like Midna, Ezlo, or Ravio & Hilda, as well as their redemption arc (before any of them came around). He also represents two of the biggest motifs found in Zelda games - that of the dreamed adventure (Link's Awakening, Phantom Hourglass), and the parallel, bizarro-Hyrule world (Link to the Past, Oracles, Link Between Worlds). Not to mention, he represents the flavor and personality of what is arguably Zelda's most iconic locale, the Lost Woods. As well as simultaneously representing Zelda series' ubiquitous woodland races, such as Deku, Kokiri, Skull Kids, Koroks, and Kikwi. Isn't it weird that - out of all of Zelda's rich catalog of fantastic races - we only have one non-human Zelda rep so far, and that non-human is a Gerudo who looks exactly like a human?
Skull Kid is such a perfect, inspired amalgamation of all those ingredients that make Zelda unique, and an essential part of the Hero of Time's legacy, who founded Zelda representation in Smash Bros. in the first place. With Young Link back, it seems almost a shame not to let him fight his own old nemesis one more time (he never defeated Ganon in his young form, while he did defeat Majora). Given Skull Kid's/Majora’s Mask’s recurring status in the series, his role in concluding the Ocarina of Time saga, his enduring popularity with both fans and Nintendo staff, and widespread recognizability, I think he's something far more than a bandwagon character. Skull Kid is essential.
