Well, for starters, Sakurai has Namco working on the game... and Namco has more experience in making fighting games than Sakurai does. Why waste time purposefully making more clones and keeping Toon Link a clone? It isn't like Melee where Sakurai made clones in the last minute to buff the roster because he had only one year and 6 months to make the game on time for the Gamecube launch. It isn't like Brawl where Sakurai made/kept clones in the last minute to buff the roster because he spent too much time making Subspace Emissary.
Namco is working in the game, but who is to say they are working in the roster of the game? Namco is well known to be masters of netcode, with their games having great online features, so I am fairly sure the reason Namco was contracted by Nintendo to work in the game is to improve the online experience in Super Smash Bros, which seems to be the focus of the games, as opposed to local multiplayer, like it was in previous iterations.
There are obviously time constraints and there is just so many characters you can add to a game in 2-to-3 years of development. There are so many things in Smash besides the characters, like the various completely different stages (most fighting games have stages which are only different in the background, Smash ain't like that), various different modes, character balancing, online features, etc etc. The roster in Brawl was already quite big for fighting game standards and it will be even bigger in Sm4sh, obviously.
So, my point is, clone characters shouldn't get as much hate as they get. Sora Ltd put they in the game as a bonus. Would you people prefer to not have Falco, Ganondorf, Toon Link and Lucina in the game just because they are clones? I sure as hell wouldn't. Even as clones, all of these characters, including Lucina, have their unique features and minor differences in their gameplays. None of them are 1:1 copies.
I am grateful Sakurai and his team are willing to have a little more work to add a few fan favorites to the game, even as clones, instead of simply ignoring them, which would be a far easier thing to do. If you don't like characters like Lucina, then that is fine, to each their own, but you will have to deal with it. Clones are a thing since the first game in the series. It is time to get used to them.