Ah, I'm glad someone finally made this thread.
Anyway, I think the Water Temple is heavily overrated and criticized, much like a lot of other things in Ocarina of Time, such as Navi. For the record to all of the fans that don't like it, it isn't the only water dungeon in the series. Great Bay Temple and Lakebed Temple also have annoyances, but people hate the Water Temple because of the water levels. It's also kind of annoying to constantly change boots in the 64 version since the pause menu loads a bit slow, but this isn't a problem in the 3DS version.
Personally, I think it is just a little annoying. It's very annoying on your first play through since you don't know where to go, and you'll be tampering with the water levels constantly to go further. However, after you've memorized it, it's pretty easy. I still think the boot changing in the original is annoying, though. All in all, yes, it is criticized way too often, but then again, a lot of other things from Ocarina of Time are.