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?