It's not as annoying as much as it's vastly open. It's a kinda non-linear dungeon. Well, the first part that is. So, you gotta get 3 keys and you can get them in pretty much any order you want, however, they're scattered throughout the entire dungeon and it's a pretty huge dungeon with 3 floors and 3 different water levels so in a sense 9 floors that you have to explore and you probably have already gotten one of the keys and don't know it, so you end up double checking a key and never checking another.
Another bad thing about it is that the Iron Boots, as Nintendo have said, are broken. They should have been an item as they have said numerous times as each time you use them, you press start, go to the equipment subscreen, put them on, go use them, (which is normally for about 2 minutes at the most) then do the process again to take them off, then do it again countless times. If they were an item in this dungeon the stress and annoyance would significantly be lowered.
However, I like the first point. For me, it's a good thing, it really brings out the exploration level that Zelda is meant to be known for. It raises the difficulty of the dungeon, although some people think that it's a bad thing because it's TOO difficult. It's not difficult as much as it's time consuming and people nowadays are lazy. C'mon, admit it, I know I am. Water Temple in OoT is one of my favorite dungeons to date. I know people are going off about how they hate water-based dungeons, but for me, they're one of my favorites because they're the hardest.