Despite point that BotW is great game, if Nintendo would make sequel for BotW I would like to see few things better done with my biggest complains about game:
-Rewarding system. For over 90% side quests in game like reward you get rupees, in past Zelda game you had heart containers, bottles, masks, upgrade capacity for bombs/arrows...here you know you will almost certain get rupees for every done side quest, that's very predictable and boring and was killing my desire for side quests. Similar goes for world quests/puzzles, you know at end of those quests you will discover onother Shrine. Same goes for Shrines also, another shrine automatically means another Orb for health or stamina upgrade. Maybe it would be much better that orbs are not linked only to the Shrines, that thorugh side quests you could also get a heart container or a stamina upgrade part, or more often weapons and armor instead of almost certain rupees, and that every world quest/riddle does not end with a new Shrine.
-Bigger variety of enemies. Not much to tell about that.
-More dungeons. Not much to tell about that.
Personally I would love that next 3D Zelda be mix of BotW and older Zelda's with smaller but more focused world.
Also I could easily see Nintendo doing Majora's Mask sequel for BotW.