I would LOVE to see the Lynel, loved that monster! He always killed me though! XD
I loved the ocean in MM, it was one of my favorite places in that game. But I think the only reason why I loved it so much was that I could swim in it, I think the best way for the ocean to work is you being able to swim fast with boosts like a zora in MM, and the ocean having lots of treasures to find in it would keep me entertained. And they would also have too have a limit to how far you could swim... I wonder what kind of limit they will(or would) set... (ie, pollution in MM, the king of red lions in TWW)But I hope there are no invisible walls, I hate those.
The museum idea sounds interesting, but I don't think it would work. This game proven to be first in the timeline, the only way it would work is if that they were more of easter eggs then actual artifacts, and replace museum with a town as Justin already suggested. But I also love the idea of interacting with enemies, like The serpent said. But what would happen if you could see a fortune teller? sorta like TP, but instead of heart containers, its your next life.
I agree with almost everything else on your list: Octoroks, a new instrument,
a magic wand would be lovely, I love tingle to the bits and pieces, (no boss returns though) EXCEPT I would not like to see a new shield design. The shield design I think is important to this game, if you notice is not a bird on the large door where you fight Ghirahim(pretty sure thats how you spell it), so the shield design might play pretty big role in this game.
My own ideas would be for the gerudos and kokiri to return, since its a prequel I think they could tell the origins to these races, it might answer questions about these races too. but, to be honest, I also just loved them! Seeing them return would make this game better then it already is.