Link has a original moveset while Ganondorf does not. So there would be more of a reason for wanting Ganon because of that. Also, in All Star Mode in the previous games, Ganondorf was listed in the late 90's section of the cast which means Smash doesn't count Ganondorf as Ganon from the original Legend of Zelda from 1986. He has appeared in more games than Ganondorf, so he deserves to get in as much or more than him.
My point is they're the self-same person in different forms. This is supported in Zelda canon. Even the more recent BotW makes note of this detail that in the past, Calamity Ganon took on the form of a human, but not this time around.
"The Demon King has been defeated countless times by heroes in the past. He is thought to have been resurrected after many years. Leading a demon army, he invades Lesser Hyrule, seeking the Triforce." (Hyrule Historia, p. 106)
"No longer bearing any trace of the man known as the Great Thief, Ganondorf, he opposes Link in the form of a demonic beast, bereft of intelligence." (ibid., p. 106)
"Extraordinary. You stand as a paragon of your kind, human. You fight like no human or demon I have ever known. Though this is not the end. My hate . . . never perishes. It is born anew in a cycle with no end! I will rise again! Those like you . . . Those who share the blood of the goddess and the spirit of the hero . . . They are eternally bound to this curse. An incarnation of my hatred shall ever follow your kind, dooming them to wander a blood-soaked sea of darkness for all time!" (Demise, Skyward Sword)
"However, the destruction of Demise was not the end of the battle. It was the beginning of a curse: a never ending cycle of the reincarnation of the Demon King, whose hatred for those with the blood of the Goddess and the Spirit of the Hero is everlasting" (Hyrule Historia, p. 76)
"Ganon . . . This beast was once of the Gerudo . . . Once human. He was called Ganondorf! King of Darkness, ancient demon reborn. The wielder of the trident!!" (Princess Zelda, Four Swords Adventures)
"Once known as the King of Thieves, Ganondorf Dragmire used the power of the Triforce to become the beast, Ganon." (Nintendo Online Guide - The Legend of Zelda)
"Though 'Ganon' is also a nickname for Ganondorf, here it refers to the beastlike form adopted by the thief following his transformation. The Demon King resembles a giant boar." (Hyrule Historia, p. 90)
"A design sketch depicting Ganondorf’s phantom. Ganondorf never appears in the Oracle series, however. Only his beast form, Ganon, is seen." (ibid., p 169)
"Ganon: No trace remains of the human known as Ganondorf." (ibid., p.121)
"The history of the royal family of Hyrule is also the history of Calamity Ganon, a primal evil that has endured over the ages." (Impa, BotW)
"Ganon was born out of a dark past. He is a pure embodiment of the ancient evil that is reborn time and time again . . . He has given up on reincarnation and assumed his pure enraged form." (Zelda, BotW)
Ganondorf is Ganon, and Ganon is Ganondorf. There are different forms he takes, and this is even seen in both OoT and TP where he has a human form and beast form. Thus, if the developers decided to introduce the beast form that resembles a boar, they could. All I'm saying is they could just change his appearance, his name, and his moveset.