Making Toon Link different would mostly be for the sake of differentiating him from adult Link.
If there was no adult Link, you'd still probably give him the boomerang, the bombs, the bow, the spin attack, etc. Those moves are representative of Toon Link as well. It's not as if Toon Link feels wrong having those items and that's why people want them changed, it's just that his specials aren't that different from regular Link.
Now, I will be disappointed if they don't at least, for example, make his tether the Grappling Hook instead of the Hookshot. And really, the Deku Leaf (one of the most used items) or the Skull Hammer would be great (the animation on the Skull Hammer is just great). But the only one that I think is "wrong" for Toon Link not to have is the Grappling Hook because of how much more prominent it is than the Hookshot. The bow at least has significant story importance.
I do hope they make his specials work more differently though... give him the mobile Hurricane Spin on the ground, for example! Or add effects to his arrows.
By contrast, changing Ganondorf would be for the sake of representing the character, which is a very different motivation. Ganondorf as he is in Melee/Brawl just doesn't do the things that Ganondorf does. The changes to Bowser and Pit, I think, are the more useful examples since Bowser shows they're willing to shake things up significantly (to make him better) and Pit shows they're willing to replace acceptable moves to reflect the character better. And both of those reasons to change a character are relevant to Ganondorf.
De-cloning him is related as well, but Falco, Toon Link and Luigi are much more closely related to who they're clones of - so reworking their whole move sets wasn't on the table anyway. Toon Link already does Toon Link things. Luigi does mostly the same things as Mario (and there's still hope for the Poltergust...). Falco they do have some freedom with, but it's not like he or Fox fight hand-to-hand in the first place, so his move set also isn't "wrong".