It flirts with breaking one of the cardinal rules of puzzle design, which is to ensure that there isn't too much of a gap between the player figuring out the solution (the fun part of puzzles) and executing that solution to receive the extrinsic reward. If there is too much of a gap, the player ends up feeling like they're just going through the motions to get the game to recognize that they've solved the puzzle, and that gets frustrating and tedious.
In the Water Temple's case, the core puzzle that defines the whole temple is setting the water level. The problem, however, is that that's a pretty easy puzzle to solve, once you navigate to the three adjustment points for the first times: You see something you want to reach, you determine which water level you need, you go to the adjustment point to get that water level. Depending on how lucky you get in your exploration, that can mean you end up doing a bunch of trudging to get to the adjustment points every time you realize you need a different level. That means you spend quite a bit of time executing the solution after figuring it out, which is annoying.
That said, the temple is pretty well-designed to guide you to be in the neighbourhood of each adjustment point when you need them, so it's fairly intuitive to end up following a route that doesn't require all that much tedious trudging around and therefore doesn't run into that problem. That means that a lot of players are never going to have a problem with it, while others might if they wander off of that deceptively linear route. I think this is why it tends to be a bit polarizing: people who had to do a bunch of backtracking because they made some unlucky mistakes found it annoyingly fiddly, while people who didn't like it.
This is my signature. It exists to keep people from skipping the last line of my posts.