The one problem I had with the game was that you had to buy items, or rent them, as opposed to finding them in dungeons. I appreciate that it was as flexible as possible, tackling dungeons in whatever order you felt, but it didnt make it feel as rewarding overall. When you're as bad at Zelda games as I am, you die a lot, so most of my time playing until i completed it was rupee hunting.
Apart from that, great game, fantastic story, and brilliant item mechanics.