So he needs "muh recency?". Why do you need to be more relevant if you're already from one of the most iconic Zelda games ever? (also he was in Twilight Princess.)
Was Wart a popular character from the best Mario game or even remembered by most (not to mention this is just a reskin of Doki Doki Panic.) This is a bad comparison.
So they deserve a better chance because they are newer? "Muh recency". Seriously, saying it makes NO sense is really exaggerating.
The Skull Kid in question is the form he appeared in in Majora's Mask. The appearance in Twilight Princess helps in hardly anyway to the point that it's basically irrelevant.
Wart was certainly not from the most popular Mario game. However, saying Majora's Mask is the best Zelda game is completely opinion. So that point is invalid because it's only opinion.
As others have said, Skull Kid or any character from that far back have basically zero chance unless their popularity or importance to a series are as potent as K.Rool for example. Skull Kid is not even close.
I'm not bashing your point here, but I'm fairly sure Mewtwo has always been popular.
Regardless; both Isaac and Shulk are deserving of a spot. Golden Sun's a very underrated series and one of the most popular IPs not yet given fair representation in Smash, and Operation Rainfall was a huge movement that showed the power of the internet and the fans.
Why can't we have both?
I agree. Mewtwo has always been popular. However, his chances for Smash skyrocketed since he got the Mega Evolution, so a lot of his Smash Popularity (or his popularity in general) was boosted because of it.
I think some users on here believe that I have the notion that only new characters get in. That's not true. However, think of it this way. We've never seen a character from an established series get in if they aren't substantially important. This is why right now, if your name isn't Roy or Chrom, you probably aren't getting into Smash Bros. Or if your name isn't Mewtwo, you're not the new Pokemon.
For example, why (at this moment in time) would Lyn get added to Fire Emblem over a lord that is new, or destroys her in popularity? She wouldn't. Because it wouldn't make sense. While Nintendo allows Sakurai freedom to pick who he wants, be damn sure that at the end of the day, Nintendo likely has Veto Power. If Sakurai picked a load of characters out of nowhere with borderline ****ty reasoning, I'm positive Nintendo would tell him no.
Again, another example. Without any reason to do so, Sakurai adds Wart. There are no re-releases planned for Mario Bros. 2. Why the **** would Nintendo be okay with that? They wouldn't be.
Smash, at it's core, is created to make money. Money is made by giving the fans what they want, while keeping things rational. There are particular characters that will most likely never get in unless there is a heavy focus placed upon them, whether it's a remake, or something else. It's just common sense for business and marketing.
On the flip side, characters that play supremely important roles to a series (like K.Rool), could likely get in because of a combo of popualrity and the potential to make Nintendo a **** ton of money. This is a big reason why I believe that the "leak" is true, because if Smash 4 turns out to have the chance to have a match up of Mario v. Sonic v. Mega Man v. Pac-Man, many many many many many people are probably going to poop themselves.
Project Rainfall and Xenoblade have earned their spot in this coming Smash Bros. Not to mention I fancy the idea of how unique Zael and Aeron can be as characters. 
