I'm doing this one because It'll probably be closer than OOT vs TP, so... That's it.
Mine is Majora's Mask. While the game isn't as long, I prefered the parts between dungeons (Except the Great Bay) over the ones in OOT, and I prefer the dungeon-design itself a lot more.
Plus, the bosses are miles better than Ocarina of Time (With the exception of Ganon/dorf) IMO.







