During a recent Iwata Asks interview, Zelda producer Eiji Aonuma talked about Majora’s Mask and its original form. As opposed to counting down the same three days continuously, the timer was originally going to last a week.
Aonuma talked about development of Majora’s Mask, as well as past titles, in relation to their original concepts. The game initially consisted of reused Ocarina of Time dungeons and the time limit mechanic.
The developers thought about the frustration of a week-long timer and considered shortening the amount of days. Thus, the three day system began. This decision was made in order to create a compact and replayable world, which is what Majora’s Mask came to be known for.