I think one of the things that makes a Water Temple so interesting, and in a few cases difficult, is the intricacy they have within them. Usually a Water Temple, or anything closely resembling one has some element that makes the dungeon unique. In this case, with the Ocarina of Time Water Temple, we saw the level design. Multi-leveled with an incredibly complex water mechanic. Along with the level design itself, Link, as well as the player is presented a challenge in the form of one of Link's most incredible enemies.
Dark Link.
A challenge standing alone out of any other boss. The amount of creepiness you feel when you first walk in to the room is..palpable. Without the proper knowledge of this enemy, he will most likely mess you up without any problems. It's a creepy situation, being presented with a copy cat Link. Doing everything he did, every move he made met with the exact same sword swing. And in the end, when you defeat him, it was one of the crowning moments in the game, almost as great as earning the Master Sword for the first time.
Along the other games within the series, the Water temple is met with hesitation, as well as admiration in its design, enemy content, mechanics, and the overall flow it has in between the games. It connects you more closely to the task at hand, allowing you to have a great sense of accomplishment after you complete it. It's going to be interesting to see if SS has a Water Temple, and if it does, we'll have to see if it compares well with the others in the Series.