the water temple is my favorite temple. At first i hated it but then i noticed that for some reason i enjoyed that temple more than probably all of the others in the game. And it's not nearly as hard as people make it sound! The first time or two you do the temple it's a little hard, but now i think i can do the entire temple without even stopping once. i've pretty much memorized the whole temple.
Every time I run through it I tell myself don't forget the key below the first water change point but I always do. Once (but not my first time) I didn't use my first key for the tower (I forget where i did use it) and made it so I needed keys but couldn't get any so I replaced my ocarina with a bottle and deleted that file. If you don't do that it is fairly easy.
It's the one temple I don't remember the layout to, even on my 10th playthrough!
I think it's the fact the rooms are so similar that it's hard to distinguish between them. The forest temple is the hardest puzzlewise but it's less annoying.
I guess experience is the key to conquer any difficult temples in the Zelda games particularly Water Temple. At first dealing with this temple my auntie found it hard at first like "where's the keys in this dungeon". Overtime I found Water Temple massively easy as my experience grown in the temple.
[Beginning of Time] Hard <-------------------> Easy [Currently Now].
I agree with Chuggaconroy (One of the most popular youtube LPers who's currently in the middle of a Majora LP[let's play, for those who don't know]) that the water temple isn't as hard as it is long and tedious. Because, I swear to god the Majora WT was WAY harder than the OoT.
I think Foerer's Wind (Teleporting Spell) was designed for dungeons like the Water Temple. So you can warp through the dungeons. I found the Teleporting Spell quite useful in some ways in the game. Foerer's Wind rock, I'd say.
The trick to the water temple lies in the central tower/column whenever you enter into it. When you can raise the water to the mid level point, do so and one of the blocks will float up with it. Go under that block and go through and boom, problem solved. Most people get stuck in this part so as long as you remember that and just go through the dungeon its a walk in the park... Aside from the hall of whirlpools... that was annoying to me and extremely tedious to get through.
The original version is a bit harder because it lacks the colored lines leading you where you need to go. It is more annoying because the interface involved with putting on and removing the iron boots was not as smooth. You had to pause and equip or unequip them constantly.
However, even on the original, I didn't think it was that bad. The only annoying thing is that there were some keys on one level which you had to access through doors on a different level, so it is not always easy to track which ones you should have gotten at each water level. If you aren't familiar with it, it is easy to get to the end and realize you are a key short, but you aren't sure where you missed it.
Whatever annoyance this was, the the coolness of changing the water level and the Dark Link encounter made this a great dungeon.