To be honest, I think his slowness in Smash is a counterbalance to his attack strength, which is easily the highest in Smash.
Ike is also shown to be much faster in the Fire Emblem games he stars in and even has a high Speed stat, but is quite slow in Smash as a result of being a heavyweight. Ganondorf is no different in that regard.
Pretty much every character claps when losing, though there have been a few exceptions, so I guess Ganondorf could be one of those.
The sluggishness is, once again, part of balancing as heavyweights tend to have slow but strong moves. Ganondorf even hits harder than most heavyweights, so being slow is a necessity lest he risks being overpowered.
He does retain some of his villainous vibe, but I agree it is toned down in Smash. Even in the SSE in Brawl, while villainous, he is not as ruthless as he is in his games.
This toned down portrayal is actually closer to his Wind Waker personality, where he is more honorable, calmer and cunning, contrasting with his ruthless, brutal nature in Ocarina of Time and Twilight Princess.
Wind Waker is the only game where Ganondorf shows some remorse for his actions and actually spares Link and Zelda's lives when getting their Triforce parts. He still retains some ruthlessness in the sense he will do anything for his goals, but he's much more subtle about it.
This portrayal does make sense as he was defeated in the past by the Hero of Time and is less prideful to the point of not underestimating his foes.
However, when he gets the whole Triforce and is about to have his wish granted, only to be interrupted by the King of Hyrule at the very last second, he snaps, laughs insanely and reverts to his old brutal self, engaging Link and Zelda in one final duel to the death.
Considering the composite nature of the Zelda characters (notably with Zelda having her Twilight Princess design, OoT spells and Phantom from Spirit Tracks or Sheik transformation), it's not too far fetched to see him in this light. Wind Waker was my first Zelda game, so I tend to have that game's interpretation of him in mind more than the other games' portrayal.
On the 3DS version, he looks better, I must say. Though that also applies to a few other characters, like Link.
Also, they had to make new models for all characters due to developing in a HD system. Simply porting the Wii models wouldn't be viable. The design is still based on Twilight Princess, though.
I agree the model could look better, especially regarding facial expressions, though the more colorful textures remind me of Wind Waker, which isn't a bad thing, honestly.
The facial expressions issue is a bit ironic, as he also had some goofy-looking faces in his original games. Like these:
I couldn't take that moment very seriously even though he was threatening Link, Zelda and the Sages' descendants.
The face he does when taking the final blow in Twilight Princess is also kind of funny.
Anyway, I agree that his Brawl model looked better and that the Smash 4 development team could have done a better job when doing Ganondorf's HD model. Though those flaws are impossible to note during normal gameplay and require specific camera angles, so I don't think it's that problematic. Could have still been avoided, though.
Then again, a few other characters also have animation problems, like Rosalina where her legs sometimes stick out of her dress and you note they aren't fully renderized and actually disconnected from her body. In the 3DS version, Dark Pit has a bug in the grab pummeling animation where the bow detaches from his model, something that doesn't happen with Pit.