This is an idea that I had many years ago, but I don't think that I ever shared this in detail on this blog. It was about a Master Quest version of Twilight Princess. I fantasized a lot about this in the past and these fantasies now came back while playing Twilight Princess HD, where again they missed the opportunity to create some true 2nd Quest, instead of just doing the usual Hero Mode option.
Anyway... similar to the 2nd Quest from the Wind Waker you get to keep the Ordon Clothes. One of my main visions was Link fighting Darknuts in his starting outfit - this was basically the signature of this mode. Though in hindsight I don't think that the Ordon Clothes look that good, but it still would be nice to have them as an option, where wearing the clothes could cause double damage / a blue heart meter (instead of some amiibo doing this). Additionally there would have been a way to keep using the Wooden Sword for an even greater challenge. If the Wooden Sword burns, you can buy a new one in a shop. All the game needs would be two more inventory slots for this, one for the Ordon Cloths and one for the Wooden Sword. And in combination they would act like the Cursed Ring from the Oracle games.
Now, in the Master Quest mode the enemies would be completely re-arranged to add a Cave of Ordeals-esque challenge throughout the entire game. This would include all Poe Souls, where they would appear as early as the Forest Temple to annoy the hell out of you, because you can't beat them yet and you need to backtrack later on. Darknuts would already appear in Lakebed Temple and the miniboss fight in the Temple of Time would feature multiple Darknuts instead of just one. And even on the overworld things would be more difficult, e.g. armored Dinolfos appearing on Hyrule Field. The only place, where I probably wouldn't mess with enemies all that much, is the Cave of Ordeals, because that's already good enough.
The dungeons in Twilight Princess are arguably less open for modifications than the ones in Ocarina of Time, because they follow a more linear and scripted flow. Still, it's possible to partly change routes, especially in dungeons with two wings like the Lakebed Temple, Arbiter's Grounds, City in the Sky or Palace of Twilight, where you basically would let the player explore the other wing first. Or in Goron Mines the central room with the moving magnetic cranes could be used to change the course of the dungeon. There are possibilities. In the Temple of Time you could even twist the whole concept by giving you the Dominion Rod right at the start and having to move the statue all the way up, instead of down, in order to get to the Boss Key...
In addition to tougher enemies and modified dungeons it would also be interesting to have the sidequests changed somewhat. I already mentioned the redistribution of Poes, but in the least I would do the same for the Golden Bugs, so that they are not as pathetically easy to find. Try to hide them somewhere.
In any case I hope that Ocarina of Time won't be the last Zelda game to ever see a fully fledged 2nd Quest again. I'm getting bored of the lazy Hero Modes that Nintendo keeps throwing at us.