Perosnally, I feel like the least of zelda's issues is the alleged dugeon-field-dungeon formula. I feel like the problem is with other game structures.
It's larger game structures that really really irritate me. Now in spite of a couple bugs I DO think that for a lot of reasons SS is easily the best game since MM, but seriously I get that the game is about the triforce, but why the hell do I have to do every God damn thing 3 times. I need to go to the 3 dugeons, doing 3 fetch quests to get into them, searching for the princess, and unlock the three areas, so that I can later do 3 fetch quests before I have to play 3 songs to enter 3 silent realms to get into 3 dungeons, after which I have to chase 3 dragons to learn 3 parts of a song so that I can go and enter the silent realm again and then enter a dungeon where I have to collect 3 pieces of the triforce. I mean REALLY WTF. WHY SO MUCH 3.
This enclosed map, non-interconnected overworld BS needs to go. Seriously 4 games now with that ♥♥♥♥ is more than enough to know that it is a fault mechanic. If I can't explore at least most of the main areas ( I can understand why some hidden areas are off limits) there is a problem. The game should not need to limit me by only allowing me to travel down one path. A much better way to do this is to show me all 3 paths, but have a tree that I can't cut down not too far from either of the other two that I'm not intended to go down. Items, especially in Zelda act great as keys. There is no need to put arbitrary restrictions in, not having a hole in the sky open, when a simple trigger would stop me from exploring further than I am supposed to, but still give me freedom. I want CHOICE.
GET RID OF THE ANNOYING SIDEKICK. Phi was funny, I actually enjoyed her as a character, that being said, she is the worst sidekick ever. She ruined so many puzzles, said so many obvious things, and lacked a lot of actually useful functions, storing side-quest info. She was Navi on steroids, and not in a good way.
More tactical combat. SS was actually pretty good about this, but it was very present in some areas, and not enough in others. I really liked being able to manipulate how I fought my enemies with things such as Time shift stones. There were a couple of stones in rooms with enemies that were only around in the past. As a result, I was able to manuever the enemies in and out of the stone to make them easier to fight, or it was harder if I messed up. More scenarios like this would be great. Put enemies that die in lava on a platform over lava, so that you can kill them. Add statues that breath ice breath and damage/freeze you and enemies. Maybe you can climb onto a frozen enemy and reach a ledge that would lead you to a hidden area, or let you skip a few rooms in a dungeon. People always talk about non-linearity, but what they really want is choice. So give us more choice in combat. Like I said SS, with it's sword fighting and decent amount of tactical items really helped, but take this much much much further.
What is the likely Timeline
What I would like to believe
I honestly would rather have Zelda go back to its roots rather than it be completely changed. I mean, what happened to all the exploration that Zelda is supposedly known for? I didn't see any of it in SS.
I think that modern zelda has the right idea, but it needs to be perfected. It has the good part of older games, in that it has nonlinearity kept in its side quests. At the same time, the main story combines exploration with a more action packed linear formula, giving modern zelda the best of both worlds in this regard.
I don't feel zelda needs to change its overall formula. That's like saying mario games shouldn't be about going from level to level stomping goombas. It is a formula that works, and the smaller things are what should be changed to make something new.
And to those complaining about skyward's overworld, it's like there are three major areas (Akin to kokiri forest, lake hylia/zora domain, and death mountain) only bigger, and the sky is like hyrule field. I don't see a huge difference with that.