The items were awesome, the dungeons were some of the best, if not THE best, in the Zelda franchise, the characters had the most character development in the series,
the music was the best in the franchise and the graphics are debatabley the best in the franchise as well.
It also had the most catching plot right off the bat. But right after you get the Master Sword, it doesn't feel like it stays the same. It has little to no sense of urgency or darkness. But after the City in the Sky, it goes back to the darker feel to the plot that I enjoy so much.
I would say it has the standard Zelda problems, but in a slightly lessened form. So, in my mind, it's the best Zelda game out there.