Considering the low amount of dungeons and high amount of side-questing, I agree about the need to alter how you obtain certain items throughout Termina. Plenty of mini-games offer opportunities to switch things up in terms of time/score requirements and overall difficulty.
Ocarina of Time featured boss battles, and since Majora's Mask won't need to feature the same mode I wouldn't be surprised if something along those lines is implemented in its place.