So include Ocarina and not Majora's Mask, then. Which is better is subjective (I would say Ocarina), but which is historically significant is not, and Ocarina is one of the most historically significant games in existence.
By the way, they also snubbed Link to the Past. I suppose that's in favor of Link's Awakening. That's just trolling.
I suppose every major series could have a separate argument about which entry they picked, though. Like Sonic CD, Street Fighter, RE4 but no other RE games, Doom but not Doom II, no Dark Souls in favor of Bloodborne, which FF they picked, etc.