I guess I didn't really notice anything different in the dungeons' layouts, but they might have changed around the location of random enemies or something. I really didn't have a tough time with it; I actually beat it in one sitting last summer vacation (I remember my family was watching Despicable Me in our hotel room and I tuned out the whole movie

But I don't really recall having much too much trouble with the original one either. I beat it with no problems when I was in elementary school, and yet it seems like everyone else really had trouble with it. I remember every time my sister replayed OOT she would make me beat that dungeon, and I still see Internet jokes/memes about how hard it was/is. I think the key is just keeping tabs on the water level in the ~8 rooms connected to the center pillar room, and noting where the three song tablets are. I guess I found it to be more tedious than anything else.
What is funny though, is that I didn't mind the Water Temple, but I had a ridiculous amount of trouble beating the Tower of Spirits in ST, and no one really seemed to complain about that dungeon, or at least weren't as vocal about it. I actually had to pause my DS and take notes to figure out what directions to send Link and Zelda in. I guess different minds work differently; I think I'm just horrible at multitasking.
