I've compiled some suggestions about which characters should have their special moves rearranged since Supreme Dirt has insisted on removing side specials:
Link: Boomerang definitely reclaims its neutral special position. As an additional suggestion, how about removing the gale effect and changing the texture of the boomerang to match his 64's version of the weapon.
Game and Watch: Remove sausages, and replace them with his side special. His side special is undoubtedly more useful.
Zelda: Two potential changes can be made to Zelda. Her transformation ability can be removed, or re-mapped to a taunt, and Nayru's Love could become her down special while Din's Fire can become her neutral special. If Supreme Dirt doesn't want to use this option, I recommend removing Nayru's love in favor of Din's Fire as it is a more important part of Zelda's game.
Pokemon Trainer: This one is awfully tricky. I believe Pokemon Trainer would be severely gimped if his Pokemon's side specials were removed, and he kept Pokemon Change. So I propose that Pokemon Trainer is scrapped entirely, and the three Pokemon are given individual spots on the character select screen. Squirtle's watergun would become his down special, Ivysaur's Razor Leaf would become his neutral special and his Bullet Seed would become his down special, finally Charizard's Rock Smash would become his down special.
Peach: I believe we should open this one up for debate. I don't believe there's a clear cut answer for wheater Toad or Peach Bomb is more useful.
Ice Climbers: I'm no expert on the Ice Climbers. I would recommend swapping their neutral special with their side special for recovery purposes, but again, I'm no expert. Perhaps cutting their down special is in order?
King Dedede: Dedede's mech-hammer is generally considered to be his least useful special, so I recommend swapping it with Inhale and making Waddle Dee Toss his neutral special.
Ness/Lucas: PK Fire takes the position of both PK Flash and PK Freeze respectively.
Toon Link: To differentiate him from adult Link, I recommend keeping the bow and arrow as his neutral special.
Olimar: Re-arrange would have to be lost for his game to work. So Pikming Pluck would become his down special and Pikmin toss would be his neutral special.
Jigglypuff: Rollout should be swapped with Pound.
Let's get some character talk going here!