They could have made it so that its the ONLY weapon you can kill Ganon with, along with this list of "things" to consider - all of which would require a pre-disposed progression in the game:
You'd obviously have to find the sword, and be strong enough to get it in the first place (this is...
The implementation of the Master Sword in this game makes no sense, not to me. It's too easy to get 13 hearts and get it, but then it's relatively weak unless used only to "seal away the darkness". But when that happens, it IS very useful ... 60 damage per hit, and about 200 durability...