I think it'd be cool if all the ruins were rebuilt. Imagine having a rebuilt towns on the level of Majora's Mask clocktown, where the many of the NPC's have their own side quests and stories.
Also, I want to see underwater exploration, and a better Zora suit. IMO Majora's Mask is the only Zelda game which did swimming right, the Zora suit in BOTW was honestly quite disappointing, so maybe there can be a buffed one that's fast? Also, maybe some underwater combat to, Majora's mask underwater combat was acceptable (better then the other games for sure) but it wasn't great, like maybe the Zora tridents could be stabbed while swimming?
Also, as a replacement for Shrines, I think caves that are essentially mini dungeons should be scattered about the world, and should look different based on their location and should have different rewards.