I'd like to take a few stabs at this idea generation gig (not sure if character specific weapons are considered part of the PSA, but here are my ideas):
For Toon Zelda over Lucas, the elemental attacks seem fine, though I'd suggest that the PK Thunder effect change into a ball of pure light energy, indicating Zelda's purity and the power she combined with Link's bow in the ending battle with Ganondorf in the Wind Waker. Also, the "snake" could be... well, I can't think of anything for that.
Next, Skyloft Link over Pit, I'd think possibly changing the Bow version of Palutena's Bow into the Hero's Bow, but still have that light arrow, and changing the twin sword version into two training swords that Link would use in the beginning of Skyward Sword (though he only had one there), Mirror Shield is fine as is, but I can't think of anything for the spinning blades attack (my absolute favorite attack for Pit).
For Tingle over Squirtle, I suggest try anything that seems like it lacks magic but is still magic (Like confetti) to Tingle.
For Lord Bulbo over Ivysaur, I'd try to do away with the vine whip attack, and for the Razor Leaf, just replace it with throwing fragments of splintered wood that all TP boars must have obtained by smashing into countless barricades.
Talon over Mario - It'd be best to leave him as is, except for the fireball, turned into a thrown stone, and FLUDD into a milk dispensor variant of the talking machine on his back.
Imp Midna over Ness - Dark Magic, 'Nuff said.
For the Donkey Kong replacement and alternatives, leave them as is; they are all alike in that they use physical prowess in battle, aside from Gohdan, who adds in his laser eyes.
Again, for Zant over Falco, Dark Magic.
Wolf Link over Lucario - You have quite a bit of freedom with this one, since it's an anthromorphic version of Wolf Link. Of course, Lucario uses Psychic abilities as well as Fighting strength, so I think it's fine as is. (I know Lucario is Fight/Steel, but you don't see his hands conjure up metal hammers instead of some aural energy)
I don't know much about the Zero Two hack, and I wasn't too aware of Vaati's powers, other than being a demon of wind (from Four Swords Adventures) and almost a copy of Ganon in malevolent behavior (from Minish Cap), so I have no ideas for Vaati over Meta Knight.
You've got the right idea for the Happy Mask Salesman over Captain Falcon for his ability to quickly get somewhere else, but I've never known him to get himself in direct conflict with trained fighters. I guess try to change the effects of moves such as the Falcon Punch and Falcon Kick to resemble masks that reflect some relevance to those attacks.
I'm not sure how Ruto and Lulu could cover up the fact that they have a gun ability from the original Zero Suit Samus, but I'd suggest that when they do the normal special attack, they show no gun, and instead, act as if they shoot their fins without a boomerang effect, like a normal energy blast from their fins.
I don't think any effects are necessary for TP Zora over ROB.
I think that's about it for my suggestions. I'll try to find some new ideas as I happen to think of them.