Because Sakurai is the major creative force behind the Smash series, and I doubt there would be any addition to any part of the game without him liking the idea of it.
He added Ganondorf because people wanted Ganondorf and his body was sorta the same as Captain Falcon. And they had a spare GCN model laying around. It doesn't seem like there was ever a time when Sakurai actually intended for Ganondorf to be in the game (like if he was cut or originally planned, he wasn't). He had more enthusiasm for adding Young Link than he did for Ganondorf.
Brawl, he at least seemed to understand Ganondorf is kinda an important dude and should be featured more heavily and made more unique, but with Smash 4, now we're back to Ganondorf just being a random guy on the roster and not the main villain of one of the most important series on the roster. Sheik has always held a higher spot on the roster than Ganondorf. I'm not talking about tiers, but in marketing and how much he talks about the character in outside media.
In general it seems like unless you're Bowser, the Koopalings, or Mewtwo, Sakurai doesn't particularly care much for villains. He even took Metaknight and Dedede who started as villains and quickly made them not villains in later Kirby games.
Not really sure why that is, but villains just don't seem particularly important to have on the roster for him.
In fact, I'm pretty sure the Koopalings and Mewtwo are the only villains (and Mewtwo is arguable) added to Smash that were not added due entirely to fan demand.
Bowser - Fan demand
Ganondorf - Fan demand
Mewtwo - Because Mewtwo is awesome with his wicked voice and psychic powers and his cool movie and woosh bam psychic mind crush (seriously, this is basically what I've gathered from reading about why Mewtwo is in Smash)
Wolf - Fan demand
Koopalings - Because the Clown Car concept was cool
And Dark Pit, Dedede and Metaknight aren't really villains.