Bird statues in Skyward Sword sort of fixed Number 2, for better or for worse.
But what I liked to do in other games was actually save and quit after I get the boss key and load the file and take the warping device, rather than backtracking to the boss room :p

I didn't really have a problem with the other

What I would like to see changed is that optional side quests play a larger role in the game. Having a whole side story arc or something would make side quests that much more worth it to do

More Customizations. Skyward Sword, I feel, is a good step towards upgrading your gear and such, but there is so much more potential with it

Regarding the OP:

1. Finding the same old items again and again

It's kind of contradictory that you'd like a Zelda that gives you some items, yet you want more things as you go around. I know, you're making the case of giving us the old dungeon items from the start and then having new dungeon items to play around with. Unless you want some Portal Gun into your Zelda, I pretty much doubt this will be the case (even though appreciated), as Zelda-puzzles pretty much have all the items needed covered by this point.

2. Kicking you back to the Dungeon entrance when you reload a save

I don't really see the problem. Be a man and beat it in one sitting! Backtracking makes you get better at the game.

3. Restarting from 3 hearts when you die

I agree, they should do something differently. In fact, when you retry after a death, your health should be fully refilled and have a one-time inmunity from any normal attack. Because if you died it's probably because the game is too hard, so there's a way to make it easier next time.

4. Empty Overworlds

I guess they can always trim down the amount of space you can cover in the overworld? It doesn't seem the case in the new Zelda, though, and it doesn't seem like there's anything worthwile to do around except for trimming down grass.

That out of the way, I guess I can add something to the thread. These are the things I think need to change (or add) in order to make a better experience:

Don't make Link the only hero.

It's a cliche of the franchise, but a reiterative flaw nonetheless. In Zelda games, it seems that the only one who can get work done is Link, regardless of the situation. It makes everyone else feel incompetent. Rarely, there's the strange case of Link needing someone's else help to do something (which can boil down to throwing these people into switches for you to advance). Let's switch around it for a bit. Let's put Zelda in the spotlight for some time; it's sexist that Link can be capable of everything yet Zelda can only play the damsel in distress. Link could get captured and imprisoned and the princess could go and save him (while playable, I mean).

Remove collectibles.

If later Ubisoft games have taught us anything is that we're tired of collectibles. They're boring. They add artificial lenght to a game, and for us people who do care about maximum completion, a pain in the ass. So remove all that. Pieces of Heart? Gold Skulltulas? Hell no! Just create additional (smaller) dungeons that once cleared max up your health or give you some sweet rewards. No one wants to go climbing houses just because there's some pesky Piece of Heart over there.

Allow for New Game Plus.

I'm not sure if any Zelda game has allowed this, but I guess it's time. Simply make room for some New Game Plus. Maybe we want to start the story all over again, but we want to go with OP Link from the start. Why not? It breaks progression you say? Alright, simply remove the required key items and make them grab them again, but leave my 999 Rupee Purse where it belongs, on my inventory!

Add choices with consequences.

Simply enough, allow the players to make some choices. Imagine that you could go first to either a Goron or a Zora dungeon, but depending on which one the player might go, the other one will be harder and the story within will be different because the hero was too busy doing something else (the other dungeon). Not only this would give some nice replayability, it would also make us consider better what it means to be the Hero of Time.

(Taking in consideration the previous one) Add bad endings.

A good way to punish careless players. Fail at the final combat and you trigger a special sequence on which you discover why your inabilities at fighting the evil have brought the worst to Hyrule. Or for a nice change of pace, allow Link to become evil. Or you know, some decisions getting into nasty endings. I'll let Anouma be creative with this one.

Funny costumes for finishing the game.

A personal inquiry of mine, I love when a game gives you silly costumes (or just plain awesome ones) after beating the game. For me this is giving the game a second playthrough with my new found clothes. Closest to this one was Wind Waker, which allowed Link to go in pajamas after the game was beaten once!

I can think of more things that need changes, but this will be okay for now.

Make Link lefty again, damnit

In a perfect world, where people dont have things to or places to be, that works but not everybody has the opportunity to play for an hour or more at a given time.

True. Even then, it's still warranted that they start you at the beginning of the dungeon. Getting to where you were again is quick in Zelda, since your progress is still saved, its just your position that isn't. And getting back in touch with the dungeon after not playing for a while is especially necessary, so that you know what you're doing.

I dont think its a big deal either, i was just saying sometimes its not feasible to beat a dungeon in one sitting.

I can't always spare an hour or two to sit down beat a whole dungeon in one go, and that's true for a lot of other people too who have demands on their time such as work, school, children, etc.

Being able to sit down and quickly solve a few rooms in half an hour, then pick up where I left off when I get another spare window of time would be immensely handy. I don't need to contextualize or re-orient, I can remember what I was doing, and making me backtrack to where I was is wasted time.

I generally agree with these. Heck, I say the Zelda series needs a revolution in its game design in general. I've been playing the Zelda games since the early 90's. Wind Waker was the series' peak, though stretching itself already. I was beginning to lose my patience with Twilight Princess, then the last straw was Skyward Sword; it felt so archaic and everything it required the player to do was a chore. I barely got through 1/3 of it and I told myself I swore off the Zelda games for good. I hope that changes.

The main problem with the games is that they give off the feeling of scope but in reality it's confined and structured, which ultimately gives the player little reward for doing so many repetitive tasks. Sega's, Square's, and Konami's games are great at rewarding their players for their hard work; not so much Nintendo. If I were lead designer of the Zelda games, here are the changes I would make:

1) All the weapons you'll ever need will be available at the start. The game's design will naturally flourish from this because it gives the player more combat freedom. Think Radiant Silvergun.

2) No respawning enemies. This eliminates disruption in flow and overall annoyance. The only enemies you fight are the necessary ones you have to kill at a given time. Think ICO or Shadow of the Colossus.

3) Ditch the compulsory long distance traveling. Warp from anywhere you are instead where you choose your area after it's visited. Travel only to get to sidequests and bonuses, like the Final Fantasy games.

4) When you die, you begin where you last saved, from which you can save anywhere.

5) Multiple difficulty levels where you can keep all the money and weapons from previous game finishes, like the Metal Gear games. This gives some replay value.

6) Bigger focus on tight, concise, creative platforming than repetitive meaningless combat. Uncharted 2 fixed this from the first Uncharted and became a much better game.

DX

Oddly enough, when I first saw this mechanic in the game, I was annoyed that I would have to scavange for items to get better gear, but being able to upgrade your gear and make it different (though not required) was pretty neat and fresh to the game. In hindsight, I actually like this though it can definitley be refined

Higher challenge in everything. Deadly enemies and traps, brain-busting puzzles, treacherous lands that need careful navigation, thrilling thrills. Bring the difficulty level back up to NES standards.