Was always my favorite Zelda back when it released. Now it's the reason I'm finally going to get a 3DS.

Nostalgia overcomes reality every time.

This was, and rightfully so IMO, one of the most hated Zeldas.

- less dungeons, time limits are always bad, fierce diety too OP it made the end boss a cake walk.

Long story short, it didn;t compare to Ocarina, not by a long shot

I'm not a Zelda fanatic, though I can only assume it's the same the Wind Waker suffered (and Zelda U in the future): people were expecting something, they got something else. Majora is VASTLY different from Ocarina despite being the direct sequel, Wind Waker follows that impressive Gamecube tech demo and ended up as a cel-shaded game. Personally, having played them only recently, I though Majora was FAAAAAAR superior to Ocarina.

Both games have seen a huge surge of popularity (especially WW). I also wouldn't be surprised if Skyward Sword suffered something similar.

Reminds me an awful lot of the Final Fantasy fanbase, but I digress.

I'd argue that MM is the hardest of the 3D Zelda games, even if the last boss was easy. 

Having been a fan of both series since my childhood, they are almost exactly alike. You have OoT/FF VII taking the nostalgia crowns because they were the first polygonal games in their respective franchises. You have people who prefer only the classics. And then you have the thing where a game is the favorite over a certain period of time since its release. You even have the same arguments about how one game is "less Zelda/Final Fantasy" than the others. 

Never got the "Fierce Deity is too OP" argument. Not only you have to get every single mask to get it, but you don't even have to use it. I myself got all the masks, but didn't use the Fierce Deity 'cause I wanted to see the "real" final boss.

And the Inverted Song of Time makes the time limit a non-issue.

It did thing's that are not present in the minimalistic approach to story telling present in other Zeldas. The main and side stories were small and more focused with a lot of well writen characters. The dark themes and atmosphere took advantage of the players emotions and was appreciated by the adult gamers. 

Ocarina was new and innovative when it came out so I don't find the newly found hate for it justified just because the new Zeldas arguably surpassed it. It's like calling the original Super Mario Bros overrated because Super Mario World was better. 

Ha. The more you know.

Like I said, I'm not part of the Zelda fanbase (even though I enjoy the games), but I always thought they were similar from what I saw =P

Wind Waker was dismissed by A LOT of people back then, and today it's a fan favorite. Similarly, people dismissed FFIX at the time. Guess what? Fan favorite today.

And wasn't Twilight Princess fairly criticized at the time of release but today is enjoyed by most people, not unlike FFXII? And then you also have FFVI and ALttP taking the nostalgia crown in recent years, while OoT and FFVII are being considered "overrated"