Toon Link isn't a clone of Link. They have different movesets and abilities. A clone character is something like Falco is to Fox, whose moves in previous games had no real difference. I'd wager that Lucina's moves differentiate her from Marth and she's more than just a female version of his move set.
I haven't actually been paying close attention to Toon Link. Is it more than just speed, height and different colored bombs and arrows this time?
Toon Link is a lot faster and a bunch of his attack work differently in brawl. I know a guy who's very good with Toon Link but terrible with regular ass Link. They're still clones though with very similar attacks and move set only with subtle but important variations. Anyway, I think link is just a skin for toon link in the new one since they wanted to get rid of the almost clone character thing they had in melee and brawl.
I hope they take notes from Project M. That made a lot of strides towards making even "clones" have very unique move sets. Many of the specials were similar but almost every other attack they do is custom.