I think of it as, people tore apart Majora's Mask for not being Ocarina of Time. Like the game or not, you have to get that Ocarina of Time was one hella game to follow up on. Majora's Mask was very different. It wasn't what people wanted... at the time. Then years later, when people have (hopefully) become more reasonable, they go back to it after the sameiness of Twilight Princess and see how refreshingly different it is. Kinda like Luigi's Mansion and Wind Waker, people didn't like them because they were different. Luigi's Mansion wasn't a new Mario game, and Wind Waker had the cartoony graphics. Then later on, people saw them for what they were : great games in their own right.
TLDR: Times changed.