Think of this as an upgrade to Majora´s Mask. Or as a bit of Elder Scrolls: Oblivion in Zelda.

Basically, have every NPC do something that…makes sense. No stupidly running around persons that are there just to fill the environment. Have there be a schedule that every character lives after. Make it not only 3 days, but maybe a whole week of different actions and happenings. There´s so much that could be done with that. Not to mention that it´d make the world feel that much more alive.