NPCs get in all the time though. Heck, Zelda and Sheik are NPCs that did basically nothing before their inclusion. Ganon and Ganondorf have had (sometimes multiple) duels with you, which would have been perfect for inspiration. And while villains seem to be few and far between in this series, that's more because they tend to either be one-offs, or have a plethora of heroes above them in the hierarchy of importance for that series. Ganon and Ganondorf don't have either problem as seen by the fact that there are technically only two other characters that were added alongside him. Also, he's one of the most iconic Nintendo villains, second only to Bowser. It may have come at the cost of another character like Pit or R.O.B. or something, but the idea that he wouldn't have been added in Brawl seems highly unlikely, and the idea that he wouldn't have been added at all is unfathomable to me (though that idea may have been a result of a miscommunication).
And Ganondorf's skills in Smash are based upon OOT anyway. But that wasn't enough to get him in.
Also, Zelda/Sheik are a special situation. It was both or nothing. Their entire gimmick was "transformation". Sheik also was fortunate to have a chance at the time, as Sakurai can easily figure out ninja-based gameplay. Look at how well she flows even without Zelda as part of it. Zelda barely had any actual abilities to draw from, and actually doesn't really use her own(less than Gnaondorf, no less, as his animations in Melee are based upon OOT, as I noted before). Zelda had games she was playable in too(albeit, non-canon) and fought also in the comics/TV show. Ganon obviously did too. Ganon isn't in Smash either way, which shows it's not as simple as you're making it.
Site note; Young Link and Toon Link, like Zelda, Sheik, and Ganondorf, were also special situations. Both were clones and wouldn't have gotten in otherwise. Toon Link wasn't just a need for a child version, but he directly used Young Link as a base to create via Melee's assets. The chances of him appearing otherwise are extremely small too. So if we remove all these special situations, we'd just have Link and maybe Ganondorf(by 4 most likely). Incidentally this is why I think the stigma against clones misunderstands why we even have such a good roster to begin with. We'd have lost a major villain without it. Also, Young Link and Ganondorf's core reasons for getting in were "we have enough time for some clones." This is also related to Luigi, Ness, Falcon(maybe on this one only), and Jigglypuff. They had extra time to make more, using someone else as a base in Smash 64. Brawl did something similar, though it had more plans for clones(Toon Zelda, Toon Sheik, the return of Roy and Dr. Mario) too. 4 also had its "last-minute clones". Ultimate seems to be the only game where clones were planned from the start as is. Since the roster was finalized fairly early on, in 2015. Making it so the only character planned later on before the Fighter's Pass was the first DLC, PP(a fun bonus one).
Being iconic clearly wasn't always going to matter enough. There's more situations than that. The most iconic character in any particular game isn't always the most likely(otherwise we'd have Slime and Spring Man(and/or Ribbon Girl), second or first character either. He clearly focuses on the player character as much as he can, and Nintendo has shown to agree. As they chose Hero. We don't know who Sakurai directly would've chosen, but honestly? I'd have seen him going for Hero too, since he's not just easier to make for a moveset(since he has multiple easy animations to borrow from), but the protagonist can often be easier for someone to work with for a first character. The only time that matters less is a fighting game, due to having a different cast layout, and we've started with the mascot character in almost every case(Min Min is the sole exception, and Nintendo chose her anyway).
Ganondorf either was going to still be a clone via his TP design in Brawl(if lucky) or would've come in at 4, IMO, when there was good inspiration for a flowing moveset. His moveset abilities don't actually flow in canon. Ganon is not playable, so there's no point in acting like him existing as iconic matters. They're different versions of the characters in the end. Hell, Giga Bowser is more playable than Ganon ever was in Smash, and that guy's a Smash OC anyway(a very odd Smash OC, but still actually was created for Smash first. Odd thing is Giga still hasn't made a cameo in a Super Mario game anyway. Though I think he would've made one at best in Super Mario Maker if he was a properly playable, and thus, got an amiibo).
Me too. I think it would be cool if she got a third jump since her special movement ability in Super Mario Run (her only playable platformer appearance) is double jumping.
She's in Super Mario Maker too, but it's just a cameo. Worth noting is that it's a "main" game, so it counts. Now why on earth they didn't bother adding Waluigi to Super Mario Run is a good question.
I didn't see her neat jump in SMR, though. Got an animation?
That's probably the reason, but it still feels really random. I think making the initial barrage from the Three Sacred Treasures more focused would have been much better.
My other guess is he's allowed to change Pit massively because he reimagined him, whereas he has to keep many characters nearly the same otherwise. Some isn't even about choices either, but nobody got a severe overhaul either way. Some got quite a few changes, but it's still the same core moveset(which is what he means by alienating players).
I'll just note that it's obviously we'll never agree on the whole Ganondorf thing, but it was worth pointing out how all the Zelda characters except Link are very special situations. Him being iconic was not the core reason he got in. That just helped.