I don't think it was hard... well... maybe yes... the very first time I played through that dungeon, it took me like 3 or 4 hours to figure it out, and still today, it takes me a couple of hours or so. But I didn't found it to be annoying, it was hard, but not annoying at all. In fact, I thought the Twilight Princess' Water Temple was a bit harder than Ocarina's. I liked the fact that you needed the iron boots and it's the only part in the whole game where they are really necessary. It was a bit confusing and time consuming, but not hard.
The only thing I think Mr. Anouma could fix is Dark Link... man, that sub-boss was way harder than Morpha, the main boss of the Water Temple... ironically, that's the only part I used (spammed) Din's Fire a lot as a weapon.