I agree with you and don't understand the critism TP sometimes gets. There is a reason why it has a metacritic score of 95.

Windwaker: Was fun playing through twice on GC and another time as HD remake.
Twilight princess: Got bored at the end, watched someone else finish it.
Skyward sword: Quit twice, luckily came back for the sand sea part, quit for good after. Worst of the three, but yes that mining facility was great.

The over world, art style and characters were all superior in Wind Waker. Sailing and exploration were great. Wind Waker felt like a holiday on a tropical island. Twilight princess like a mediocre remake of Oot. Skyward sword like a repetitive unresponsive mess at times.

My experience with TP might have been a bit better on the GC without waggle controls, yet I don't really like the art style and the music in the Twilight Realm is grating to me.

Keep in mind that many of those reviewers you cite are ones who praised Fi as a "great source of humor," a "masterful companion," and a "brilliant addition to the Zelda series." Without wishing to jump on board the "reviewers are unreliable" train, it's always seemed to me that many flaws in Zelda games which the fanbase widely accepts tend to go mysteriously ignored by reviewers across the board.

Anywho, Wind Waker ranks at the top of the list for me. Story is the simplest, but yet the one I find most engaging, because Link is actually something of a character, with real personality and emotions. Exploration is enjoyable, even if traversing the sea can get more than a bit tedious at times, and combat is arguably the best in the series. TP probably should have taken this spot, but made the mistake of making all of the sword techniques optional, meaning that the game had to assume that the player got none of them, thereby ensuring that enemies could never get significantly more complex. Wind Waker doesn't have this problem, and so the simple counter mechanic becomes far more engaging because enemies require it later on.

TP's biggest downfall is in its design, there's simply too many mistakes for me to consider it a particularly good game. Be it the game's really, really strange character "development" for Zant at the end, the horribly drawn out tutorial section at the start of the game, or the utter grind that is all of the tear collecting sections, the truly enjoyable sections of Twilight Princess are simply too far inbetween. Some of the dungeons later on are really good, but even that is compromised by the game losing all sense of pacing towards the end and essentially throwing six dungeons nonstop at the player with little real exploration inbetween outside of having to backtrack to find some dominion rod statues.

I'd probably put Skyward Sword at second, because while I think it's got more problems than TP, it makes up for them by at least trying to do something new with the traditional Zelda story. Ultimately, though, any good will I have towards it is lost beneath some truly obnoxious gameplay design that made me want to stop playing on more than a few occassions. Repeat boss fights, horrible swimming and flying controls, an ungodly amount of required fetch quests, and some truly bland level design ultimately killed any momentum SS ever started to build.

So I'll go WW, SS at a very distant second, and then TP.

Skyward Sword for me, it's a epic masterpiece with interesting challenges, an amazing overworld and great bosses (. I feel the same way about TP but it felt little less epic than SS. WW is great as well but against SS and TP I have to put it at last.

Twilight Princess is great game but definitely has some flaws like slow start, not interesting wolf sections, and most important that 90% people will say its TP biggest flaw, empty and boring overworld. Dungeons and some places in TP are great, but you dont have almost nothing between them, just huge, empty and boring space. Personally thing I most love in Zelda games is exploration, and exploration in Zelda TP is very weak, bad and boring, thats reason why is for me one of least favorite 3D Zelda.

At least we saw Zelda U will not have that problem, Zelda U world looks beautiful, interesting and very alive, just waiting to be explored. :)

I am glad Wind Waker is getting so much love, really deserves it, it's so much charming and beautiful game with world that feel very alive. IMO only thing is missing in game is another bigger island with characters and side quests.

I think WW HD is the best out of the 3, with SS 2nd and TP HD 3rd.

The combat in WW was just far more interesting, so that I actually wanted to fight enemies. I also liked the dungeons, there just weren't enough. I didn't like the sailing in the original WW, but that was greatly improved in HD. At the end of WW HD I wanted more.

SS had an interesting story, the combat felt good most of the time, eventhough I would have preferred to play without motion controls. I didn't get bored while playing SS, but at the end I felt finished with the game.

TP HD has cool dungeons (I really like the double hookshot), but TP HD had quite a few stretches inbetween where I got bored. The combat is ok at the beginning of the game, but later it's just a thing you do because you have to. After finishing TP on the GCN I didn't feel like collecting all the heart pieces or bottles, and when I tried to replay it a few years later I didn't get past the first time you met Zant. TP HD I finished, and again I don't want to collect the things I missed (and I missed a lot).
TP surely has it's highs, but it also has too many lows, that is why I rank it last.

give me SS HD and I say SS

Twilight Princess. Amazing all the way