(This post is about Modern Zelda, not classic. Classic does /everything/ right thanks to tension in appropriate areas which is complemented by spectacular music)
But, what are your opinions on 'late inclusions' as far as villains are concerned?
My opinions on late inclusions are that they're not worth it unless the villain is a complete badass. That being said, none of Modern Zelda's late villains have been "complete" badasses - whether it's some fluke in their fight or a huge lack of tension regarding their reveal, it's simply not enough to make me feel awed by their presence. Yes, I'm talking about TP Ganondorf, Demise, Bellum, and what have you.
Is there a way to introduce an antagonist near the end of the game correctly and not make it feel jarring?
Like I said, the key is that there needs to be appropriate tension in the appropriate area. If the villain is going to be revealed at the end of the game, we need to feel awed by their presence and they need to DO something that justifies that awe. Yes, I'm saying that seeing some mystical figure before me with some backstory is not enough (Demise). So what if the legends tell of some demon who ripped the world apart? If they can't bring destruction, they're not worth my time. That's storywise. Gameplay wise, they just need to be tough. Zelda is in dire need of one hit KOs and other things. People call it "cheap difficulty" but honestly, this is the final boss. It's a test of all your skills. Do or die, nigge.
Should villains be revealed very near the beginning of the game's narrative?
Because this is Nintendo...no.
How would you rectify the 'late inclusions' such as Demise and Bellum?
Demise: I would have Ghirahim's death be more tragic - maybe make him regret his decisions - and have Demise transport himself to Skyloft and threaten to kill Gaepora or some other resident. This would create a LOT of tension. From there, I'd make SKYLOFT the battleground rather than mystical waterland (i don't care if it LOOKED cool). With the sky province ablaze, it would still be a one on one but this would give both Link and Demise more acrobatic capabilities and also provide a backdrop of Hylians running amuck without a clue in the world...which provides tension.
Bellum: IDK, Don't remember much of him except that his boss fight was COOL. There was SOME tension because it was Linebeck...but that's all really.
Would you give them more elaborate cutscenes and history?
Cutscenes - yes. After sucking up Hylia's soul, for example, I would have Demise cause a Schism on the Surface and deal severe damage to Skyloft.
History - no. Backstory means nothing if the physical entity before you does nothing.
Would you keep them mysterious until a grand reveal at the end?
In the words of Basilio, Hell No.