Seems most of the complaints people have with the games is the plot- mainly the fact that it pretty much repeats itself. Well, if it interests you, I was once working on a Zelda fanfic where Zelda (as always, a different Zelda, although I gave her a long and complicated full name) is almost captured while on a diplomatic mission when the king of the neighbouring country of Grandale (which she was ambassador to) tried to use her as a hostage to facilitate his impending invasion of Hyrule. When Impa (based on her OoT ninja version, really a bodyguard disguised as a ladies' maid) gives her the chance to run for it, Zelda is aided in her escape by a cheeky young masked thief from the slums (who is explicitly NOT Link, nor in any way related to his bloodline, I called him Rikkin) who leaps onto her speeding carriage while fleeing across the rooftops from a gang of pissed off Gerudo bandit women he stole from. After a massive chase through city streets involving both soldiers and a bunch of annoyed gerudos who hijack their horses, and a precarious duel on the rocking carriage, they escape and Rikkin sees Zelda on her way back Hyrule before returning to the slums to help take care of the gang of orphaned young thieves he leads there, only to discover they've rescued a wounded Impa. Then Impa gets involved in the clash between Rikkin's group and the Gerudo gang led by the "gangster king" of the town, who is the reincarnation of Ganondorf (who was FINALLY killed once and for all centuries before, although this guy has no memories or anything of his past life, since that's not how reincarnation actually works). That's about all I got through before I took a break. Sure, it's not Shakespeare, but I wrote it while trying to adhere to a few simple principles, intended to keep it connected to the Legend of Zelda mythos without just rehashing the same old stories:
1) Move the story beyond Hyrule (which has always been just a single nation connected to absolutely nowhere, even though several games make it clear there's a world beyond it) without just making up an arbitrary new world and keeping the story contained to THAT one instead. In this case, by introducing the political tensions between Hyrule and Granford (name subject to change).
2) Having a young male protagonist who is NOT Link but who has to take on his role (become Hero of and seek out the power of ), allowing me to keep the tone consistant and recognizable while developing him as his own character (since all existing Links are basically clones of each other). For example, while it's hardly a big deal, Rikkin wields a pair of short knives in combat because he finds swords unwieldy, has a very agile combat style bordering on parkour and loves messing around with his rope and grapnel.
3) Replace Ganondorf as the Big Bad without just making up an arbitrary new villain (i.e Vaati). Again, allowing me to define him as a new character while retaining elements that actually make Ganondorf a menacing villain. Also have an antagonist who isn't just a puppet of the Big Bad (Zant, Vaati), in this case the treacherous king of Granford.
4) Characterise Zelda as an independant young woman who takes an active role in Hyrule's affairs (the ambassadorial mission to Granford) even though she IS just the princess (her mother is the Queen) and who has her own feelings (such as considerable Unresolved Sexual Tension with Rikkin, who she can't decide if he's cool or an immature and reckless idiot). Tetra from Wind Waker was a pretty good character, but she lost a lot of her charm when they revealed she was Zelda and she spent most of the rest of the game either sitting around or, yes, being kidnapped by Ganon.
Now of course, this story was written for a fanfic and wouldn't necessarily adapt well to a game, but I like to think it's an example of how they can shake up the Legend of Zelda plot formula without completely throwing it out the window. Among the carry-on effects it would have on gameplay, I'd be most fond of giving the hero multiple weapon choices rather than "sword and shield/hidden gimmick weapon/special item which only has a single attack action", although this admittedly runs the risk of making the game too much like Devil May Cry/Ninja Gaiden. Although I thought they'd perfected the sword combat in Twilight Princess with all the neat new moves, it was actually the multiple transformation combat styles in Majora's Mask that I found the most interesting, although they could have been a bit more fleshed out. But who doesn't think the battle against Goht (the giant mechanical bull you have to chase around in a giant circular room while rolling in Goron form) was one of the best boss battles the series has ever had (don't answer that)?
With regards to some other suggestions though, I can't agree with a lot of them. Maturity for example. The problem isn't that the games are "childish" (although I don't see the harm in aiming the games more towards a TEEN audience, pretty much what Twilight Princess did to great effect), the problem is YOU'RE childish if the best suggestion you can come up with to improve a game is "blood and boobies". The Zelda I wrote for my story has a more conventional sex appeal, at one point flustering Rikkin by kissing him when he tries to hit her up for a reward for saving her, but I don't see the need to give her a Lara Croft rack; nor if I was making a game would I feel it necessary for enemies to wash the screen with arterial spray every time the hero cuts them (although I would do something about enemy corpses just exploding in puffs of smoke as they have since time immemorial- it was a great effect for the Shadow Beasts in Twilight Princess, but was too odd on the other enemies). At the core, the game needs to remain identifiably "Legend of Zelda" but it needs some new elements beyond just new equipment (they're starting to scrape the bottom of the barrel, the Spinner and the "Gust Boomerang" in TP was them pushing their luck) and new minigames (fun as snowboarding against the Yeti was, it was still just a distraction). An example of a development that DID work very well was the radical improvements they made to horseback combat in Twilight Princess, which was now extremely thrilling (especially since you were no longer simply invincible while mounted). It's probably the best usage of a horse in any video game except for Shadow of the Colossus.
Complaints aside, I still love the Zelda series. I've played all of them except those horrible CDi abominations (OK, so I never beat the first 2) and Twilight Princess was one of the top 3 games I played last year (only possibly topped by Persona 3 FES). But I still think the series needs a shake-up. Although I'd be perfectly happy for Nintendo to keep making games of the same high level of quality, I'd prefer to see them go beyond that and make each game DRASTICALLY better. While we can never again have the kind of advances that Ocarina of Time brought over A Link To The Past, I still think it's possible for Nintendo to make lightning strike again. After all, Nintendo and especially Shigeru Miyamoto ARE the greatest geniuses in the entire video game industry.