I suspect that the biggest problem with the Water Temple was that you had to push a certain block (I believe it was on the second floor) over early on. Doing this gained you nothing when you did it, but it was necessary to advance later, when you approached from the opposite end.
Failure to do this led to your journey ending in a seeming dead-end, and the only way to remedy this was to reverse your actions for about five steps (at the cost of lots of time/tedium) until you finally got behind that block and pushed it to where it needed to be, then re-did what you'd already done and get back to the opposite end of said block. Of course, there was nothing that indicated that this was what you needed to do, since corridors all looked alike and the block being out of place didn't give you much of a visual clue...
