although i wouldn't really care for things like story, quests, npc quest givers/merchants/etc, etc.
I'd rather you focus on things that capitalise off of minecraft's strengths (land generation, mobs, dungeons)
I mean I think you could make something incredibly unique just by using whats in minecraft already. The end game is reaching the ender dragon and killing it. Maybe you could just focus the direction on that. Maybe just altering a few things that lead to you making it to the dragon like:
making a sequence from sky world to nether to ender world. having to gather different items from each to progress to the next. Instead of just using flint/steel to light the nether portal you could make it so you have to acquire an item from the skyworld to replace the flint/steel mechanic. You could also reverse nether/skyworld roles whatever works best.
but that's not even needed, just leaving it open ended like it is and making the ender dragon stronger would be good enough as a basic concept.
and anything 'town hub' related like merchants, chests, healers etc. could just be left to the testificate villages that spawn and you might be able to just add a few npc's that spawn.
I'm thinking what also might balance gameplay a bit with regenerating health is having your health bars max take a hit everytime you get damaged. so even though you regenerate it pretty quickly you still have to watch your max health and make a trip back to a healer or find an item to get you fully replenished. This could be a nice spell for a mage.
subtle touches here and there i think is what'd help this mod best.