I took a closer look at the 3D model, and like for all my N64 papercraft Zelda models, I really want to preserve the polygonal look, because it looks really great on the paper models I think.
Even so, I'll have to think of something to make the head/face and particularly the hair buildable, because it's quite a mess right now... I also want to change the hands, because Ganondorf's hands are basically just blocks with a textures. I won't make all 10 fingers again though, just the thumb, like on my other N64 Zelda models.
I'm also thinking of having Ganondorf in a fighting stance, like Fierce Deity Link. He needed a sword for that, though, but in the game he just uses lightning bolts to fight Link. I think I'll give him one of Ganon's swords (from his pig-form), stretched a bit for the right proportions.