The only villains I consider better are Majora, Ghirahim, and Lady Maud, all for different reasons.
You see, when Zelda has a villain, we barely ever get to see them in action, yet we're somehow expected to know how mean they are. Not with Majora though; we got to see him stealing Link's ocarina and horse, turn him into a scrub, calling the moon down, and laughing like a little bastard the whole way through. Other villains haven't been that impressive in this regard
What's also important for the threat factor is in the villains speeches. Zelda has a bit of a problem with cliches you see, but Ghirahim struck me another way; his detailed rants on just what he's going to do to Link really showed how sick he was.
Now Lady Maud is a weird one. She had all the problems the Zelda villains usually have, but she was a real breath of fresh air from the usual DEMON KING AWAKEN TO SPREAD DARKNESS thing. A villain with a unique plan always stand out from the rest, and Lady Maud seemed to do that in a positive way. Maybe it was just proper timing, I dunno.
Now about Ganondorf. I like him much better than Ganon, I always have. The giant pig monster just doesn't hold up anymore, but a sorcerer warlord king of a mostly female race leaves a lot more room for the things that make a villain good. But alas, I find him unable to "wow" me.
And I'll give credit where it's due; Ganondorf was pretty cool back in OoT. Unfortunately, when the series lost it's sense of direction, Ganon and Ganondorf both became a victim of it. Nintendo could redeem the two and send my jaw to the floor, but I have no reason to believe they will.
]
Okay, I'll run through these villains one by one (although I can't really talk about Lady Maud as I haven't played Tri Force Heroes yet (although I am aware of the character and the story)).
Majora.
An overrated villain, in my honest opinion. So many Zelda fans adore Majora, and I can (to a point) understand why. It is a destructive, wicked, purely evil entity...but the problem is in how I just described Majora. It. You see, I don't think of Majora as a character, really. Basically, it's just an evil entity/demon inside a mask. It has no character development whatsoever. We don't even know if it's male or female (I personally think it's without gender but many of my friends think it's female). When you see it steal Link's ocarina and horse, bring the moon down, etc, etc...it's really Skull Kid who's doing all that. Granted, he's kinda possessed, but it's him we see doing all this stuff. The mask remains stoic, without showing any emotion at all. The only time we really see Majora come to light is at the end of the game.. Majora is very effective for the game in which it appears in, I'll admit. I've never been overly fond of Majora's Mask (the game itself), I've always found it to be a rather depressing game to play through (which, I suppose, is the whole point). It just feels weird, to me. It honestly barely qualifies as a Zelda game at all (no Zelda, Ganon, or Hyrule). It is a very good game...but a weird one. So, yes. Majora is a fitting villain, because it is a weird character/antagonist. I could never imagine Majora returning again and again (like Ganondorf does), it just wouldn't work.
Ghirahim.
I'm not gonna argue with you too much here, because Ghirahim is my second favourite Zelda villain. He's a deliciously sick, twisted, character. His only real failing is that he fails to follow through on the threats you mentioned. I never felt intimidated by the character at all, I never felt that he had a chance of actually defeating Link. He's all talk, basically.
I think you're right about Ganondorf, he is superior to Ganon. He just has more presence as Ganondorf and gives off a regal, powerful air. I personally think he was at his best in Wind Waker, in which he seemed more wise and broken. It was the first time I ever found myself feeling sympathy for him. Despite this, though...I do think in a strange way it would be better for Ganondorf not to appear in Breath of the Wild. The whole title screams that this is some kind of post apocalyptic world, and we already know that this game will take place in a ruined Hyrule. I just think under such circumstances it would be better for Ganon to be the villain instead of Ganondorf. An extremely powerful, wild being would be fitting for this game, I think... We'll just have to wait and see.