To be honest I think a lot of elements have to combine to give me the perfect feeling of "true" difficulty. The main quest should be a prolonged experience in my opinion, now I know quantity doesn't equate to challenge but I think they work hand in hand - having a longer main quest makes for a bigger and more of a grander take
at hand. I think both Twilight Princess and The Wind Waker had a rather nice quest time, long enough to feel like an adventure, however I'd like for more dungeons and whatnot in the future. The game should also have a multitude of side quests to compliment the main quest, I would refer to Majora's Mask here, the sheer amount of side quests really made this game something different, it felt as if we weren't just tackling one quest but several. This added a whole load of diversity and just added to experience. That being said though, I feel that we should have to differentiate away from the main quest to complete side quests. This is something I though Skyward Sword lacked, a compact overworld lead to little trailing off and actually having to go out of your way to complete non compulsory challenges.
Combat, or more specifically, enemies need to be "significantly" improved. It's not juts a case of adding to the damage they can inflict but a case of making them overall tougher. This means smarter AI, make them act tactical, such enemies could attack in swarms or use stealth etc. Another thing would be diversity, I think this is key to give any given enemy depth. Give enemies a variety of defensive and offensive options, this will allow for more strategic combat and actually make the player think. I also feel movement patterns could key to adding strategy and depth - all of the stuff I mentioned here should also be applied to the bosses aka the weak point of the franchise.
The puzzling aspects needs to become a stellar feature again, I feel it's diminished down the years and slight attempts to revive it have not been as effective as puzzles once we're in the 2D installments. Now i don't know whether Nintendo take it easier in the modern era or of they just can't transfer the puzzling side of things into a 3D perspective, but I would love to see the difficulty of puzzles, that of the 2D games, make its way into a 3D perspective. However, the top down perspective doesn't seem to be going away, which is a good thing, and that way we can still get our puzzle fix, providing the next installment nails it.
I also think advancing should be made a difficult task to go through. Within the 3d games it's a simple task of navigating your way through one area, maybe finding a specific item before hand or completing an odd job of sorts, but this doesn't go along way in my opinion. An easier way to look at it would be to, once again, look at the top down games. I would refer to A Link to the Past here, but since I've been recently playing Oracle of Seasons , I feel this would be better to go off. Even though this overworld is too compact in my opinion, I still feel it makes navigation and progression a task. One can't simply make large progress, you have to think, revisit past areas, obtain items, manipulate the overworld via the Rod of Seasons, all of which are just used to progress further. It's this kind of linking between navigation and puzzles that really add an element of difficulty in my opinion.
I'd also really like for Nintendo to add nonlinearity somewhat, which seems likely, and also make dungeons a exceedingly tougher, however this all links into what I said above. All in all it seems like what I want is a mixture between the puzzling aspect of the 2D games combined with the potential that a 3D game can bring. It's a wish that probably won't be fulfilled but I think if Nintendo put their minds to it they can easily achieve this.