If two separate versions of any other character is "unwarranted", having two separate Links makes no ****ing sense no matter how you try to justify it. It's hypocritical.
I disagree entirely. It makes sense to have two Links based on the importance that both play in Zelda as a series. Having two Links
doesn't mean that Ridley and Meta Ridley as separate playable characters makes any sense. This is because it isn't all that important to Metroid in general. Sure, Ridley has had his separate forms, but his most iconic look is the purple Super Metroid one. Link has several appearances, and therefore has two very different forms. I view it as a situation with a fine line.
In addition, while I think Dr.Mario should be in the game (as an Alternate costume), he does not have the same justification as Toon Link does. Dr. Mario may have his own series, but it is far from a major icon of Nintendo. Regardless of design, a young Link is something that is persistent in the Zelda series.
The reason I don't believe it's hypocritical, besides what I've listed already, falls back on this. Imagine Sakurai adds a completely separate second Samus. It's a completely different suit, but has the same attacks. That doesn't make any sense really. It's a waste of a slot, and we already have Samus in her most iconic appearance.
Of course, you could say that we should nix the Older Link instead. However, the older Link is one way or another the Iconic Link to the Legend of Zelda series. Most of the big console titles (SS,TP, OoT) features a Link that is older than say, Toon Link in Wind Waker.
Overall, both forms are important. No matter how you slice it, our opinions don't really matter. Toon Link is already in the game, which tells me that Sakurai is keen on the idea, and I don't see him going back on it anytime soon. Dr. Mario specifically has it tough because of the possibilities as a 6th Mario slot. For all we know, Sakurai may consider the Links an exception. It's a mystery.