I chose MM. In addition to the huge bosses, there were also two unique and challenging sub-bosses per temple (remember that vampire Gomess?), in additon to other battles like Igos du Ikana. In every battle you had to dodge constant attacks while trying to discover a weakness. I also loved the fast-paced battle with Majora's Wrath, without using the Fierce Deity mask.
The sheer variety and how they all present a challenge tided me over. In the other games that even have sub-bosses, they often become commonplace enemies shortly afterwards.