I think it would severely lessen the evil image they've set up for Ganon. I've always seen him as the most evil of any Nintendo villian and damaging that reputation would be devestating.

I do think that the Twilight is simply another name for the Dark World. Hence, why Link changes forms (maybe you have to get the moon pearl in game) like he did in ALttP and plus what does everyone associate with the twilight hour but darkness?

It would be interesting to see a new villian, perhaps a higher power, but not overwhelmingly so. As in, Ganon keeps being the King of Evil, but there is someone else there too, maybe even a peer to Ganon. I doubt Ganon would let anyone be his equal, though.

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It is confirmed, the programmers in charge of creating the Jabu-Jabu dungeon of Master Quest, were high.