Pretty easy to list the differences... Present tense if we've seen the move in SSBU, past tense based on most recent appearance
Toon Link and Young Link (henceforth T and Y, vs. Link as L) have different models with different hurtboxes
T has a unique F-smash, while Y has the same basic movement as L
T had a single hit U-smash, while Y has the three hit U-smash like L
T had unique f-air, b-air and n-air, while Y's were similar to L's
T had a stall-and-fall d-air, while Y's was similar to L's
Y has a jab infinite, while T and L have had fairly similar jab combos (although since L's final hit was changed, they may be less similar now)
Y has fire arrows, unlike L neither has item arrows that can be used for double shot arrows
Presumably each bow has different speed and trajectory properties as well
Y and T's bombs have slightly different properties (obviously L's bombs are quite different now)
Presumably they will have at least slightly different weight and speed and range (sword and Hookshot length)
Presumably they will have different damage and knockback properties on their various moves
Most importantly: we haven't seen their full movesets. We don't know what changes have been made. Their aerials were not shown at all in their character videos (it's possible they're somewhere in all the Nintendo Direct footage, but...). I would not be the least surprised to see more changes to both characters. I bet Tink has a new f-smash because of Yink's return, for example.
Compare this to Lucina or Dark Pit:
With noted exceptions below: identical size, weight, movement speed, animations, damage, knockback, trajectory, etc.
Lucina is slightly shorter
She doesn't have the tipper mechanic on any attacks, with damage adjusted to compensate (i.e. a Lucina hit is stronger than Marth sourspot but weaker than Marth tipper)
Slight differences on a couple standard attacks and Shield Breaker (but identical animations and no difference in damage aside from tipper-related changes)
Only changes seen to Lucina so far have been echoing Marth's changes (faster Dancing Blade, ability to angle Shield Breaker, changes to jab), which suggests we likely won't see any significant decloning due to changes to Marth OR Lucina from Smash 4.
Dark Pit has a unique Final Smash
Dark Pit's Electroshock arm has different damage, knockback, trajectory from Upperdash Arm and an electric effect
Dark Pit's Silver Bow has different speed, damage, knockback, maneuverability
Slight differences on a couple standard attacks (but same damage and animations)
While there is some point that would be ambiguous between Echo and not Echo, it is pretty clear that Toon Link and Young Link are significantly more different from each other than Lucina and Dark Pit are from their source characters.
