In my opinion, if you want perfection, look at Ocarina of Time- there is not one thing I don't like about that game. Majora's Mask only built upon it, and that's why they're my 2 favorite games of all time while A Link to the Past and Wind Waker are 3rd and 4th.
And the game is undoubtedly FUN, but it's not challenging in any way, and for a game to be truly perfect I need to feel like I acomplished something by the end, instead of feeling even a retarded monkey could have beaten it. The Triforce quest, I thought, was the biggest flaw in the game- I still liked exploring the overworld, but all the while I couldn't help but feel like Nintendo could have easily spiced it up.