I've seen common incorrect arguments against Skullkid, and I made a post debunking them. This is for anyone that wants to use this information to inform others that use these arguments.
Incorrect: "He wasn't popular until like a week ago!"
Correct: He was actually the winner of the biggest poll conducted before Smash 4.
http://vgtribune.com/smash-poll-2012-winner/
Probably the reason why he got an assist and Sakurai saying "I repeat, he is not playable, he is an assist trophy."
He was also later made into a mii costume. Both are suspiciously missing now.
Incorrect: "He's one off! He was only in one game!"
Correct: He is actually in 3 mainline Zelda games. MM, OoT, and TP.
At the end of MM, Skullkid says "you have the same smell as the fairy kid who taught me that song in the woods.". This implies he is the same Skullkid from Ocarina of Time.
In Twilight Princess. The Skullkid knows Saria's Song. Also TP and MM are in the same timeline.
Incorrect: "He doesn't do anything in his games! He has no moveset!"
Correct: Actually there are a lot.
Throwing a spinning Majora's Mask (it has spikes on the sides, and relates to the first phase of the boss fight).
Mask hair/tendril whip.
Dark magic
Instruments
Tatl and Tael (fairies)
Lazer eyes
TP puppets
Moon tear
Boss masks
Final smash cutscene could be Majora dropping Skullkid like a doll and then transforming into Majora's Wrath.
Taunt: butt slap.
https://giphy.com/gifs/game-the-legend-of-zelda-majoras-mask-yETcfOWMlhdHq
Incorrect: "The Moon is an assist trophy, and Skullkid can only have the Moon as his final smash!"
Correct: Skullkid has more options than just the moon. Given that Young Link's final smash hasn't been shown, it is possible that Young Link has Fierce Deity, and is being saved for when they reveal Skullkid. Skullkid in turn could have Majora turn into Majora's Wrath in a FS cutscene.
Also his assist last Smash did not have the Moon. And the moon is actually in two places in this game (MM Great Bay stage and the assist) so there isn't actually a rule that the Moon can't be his final smash as well.
The moon being an assist is also in Skullkid's favor since we've gotten assists lately that are specific to a later reveal (Klap Trap for instance).
Did I miss any?