I think Skull Kid's design should be taken from both MM and TP...
I think that he should alternate from Skull Kid to Majora...
Skull Kid:
B: Puppet Song - summons the puppets from TP
UpB: Wind Warp - disappears and reappears like in TP
SideB: Deku Nut - slams a Deku Nut onto the ground in front of him with about the range of Zamus' Dsmash but a bit more....it stuns people like Mewtwo's DownB
DownB: Majora - SK's mask wiggles and he falls on the ground lifeless...like when you run out of HP in Stamina...you know control Majora's Mask
Taunt 1: laughs
Taunt 2: does that butt thing he did when you saw him through the observatory in MM
Taunt 3: dances while playing the first few notes of Saria's Song
Majora's Mask:
B: Sun Beam - starting lag is equal to the SSB64 Falcon Punch...shoots fiery beam at the ground in front of him like Bowsers FireBreath...and can be angles with the C-Stick (but not straight up or straight down...just at angles and forward)
UpB: Dark Twister - spins rapidly like a tornado and can be angled like Meta Knights SideB but its easier to go up
SideB: Parasite Mask - with its tentacles it lunges forward and tries to latch on someone....if it does, you can control them for a while (depends on their %)
DownB: Majora - if near Skull Kid, you become Skull Kid...if not you transform into Incarnate (or Incarnation I forget...)
Taunt 1: spins and its eyes glow even brighter
Taunt 2: faces the screen and its tentacles and spikes wiggle
Taunt 3: twitches with each eye taking turns glowing while its tentacles shake wildly
Majora's Incarnate:
B: Blast Dance - shoots balls of energy like it did in MM
UpB: Twirl Dance - twirls like a ballerina so fast that he drills upwards recovery is mostly vertical
SideB: Cuckoo Dance - runs around like a chicken like it did in MM
DownB: Majora - if near Skull Kid, you revert back to Mask so you can go back to Skull Kid, if not you turn into Wrath...
Taunt 1: does the chicken dance and clucks
Taunt 2: does the robot
Taunt 3: breakdances and laughs
Majora's Wrath:
B: Wrath Top - throws out those spinning spiked tops of doom it threw out in MM
UpB: Wrath Whip - jumps up a bit and spins with its whips extended...
SideB: Wrath Wrap - whips forward with both whips and if contact is made, it shocks them like Ganon's UpB...
DownB: if near Skull Kid, your revert back to Incarnate, it doesnt work...
Taunt 1: dances
Taunt 2: floats up and laughs
Taunt 3: he raises his arms laughing like a maniac and his whip and spikes wiggle
Final Smash would obviously be the Moon...