I normally do not go into "deep analysis" of any game. As long as the story is captivating and fun, that's good enough for me. However, being labeled as a "Zelda" I had high expectations for Windwaker despite it's retarded appearance. Since the Zelda games are never released in proper order, the inconsistencies wouldn't have made much of a difference. However, Myiamoto himself screwed that up. By stating even before the game was released that "This game takes place several hundred years after Ocarina of Time!" With that single statement, he was finally giving us a proper time line, and stating that this world IS the Ocarina of Time Hyrule. As such it would be expected to have been properly connected with the previous Zelda game.
All the story told us, was that Hyrule was flooded after Link didn't return. Why did Link leave? Why didn't he return? Well that explanation we could at least hope for in a new game. It's to be believed, as per previous statements from Mr. Miyamoto himself that all Links up until this point were descendants of the "original" Link. However during the course of Windwaker it is revealed that that Link, is in NO WAY related to any of the previous Links. He's just some random kid, who even hated wearing Link's clothing! Furthermore, nothing else in the story made any coherent sense. We have never got confirmation on what happened to the Zoras, and anyone who says they evolved into the bird people with no proof other than the fact their mountain happens to have the same symbol as the water temple from Ocarina pisses me off! It's not a plausible outcome, and even if Miyamoto himself says it, I'll be pissed off at him too.
I'm just happy it appears that Toon Link will be restricted to the DS, while Wii will keep the Twilight Princess art style. It's sad that once Spirit Tracks is released (if it hasn't been already) that I will have to stop saying "I've owned and played every Zelda game ever released," but at least I can switch it to "I've owned and played every good Zelda game ever released." Windwaker was an okay game in it's own right, it just did not sit well as a "Zelda" game. Nintendo was simply using a classic game title to entice people to buy a new style of game visuals that they weren't sure people would want. Sadly it worked for most people, the only reason I bought Windwaker though was that if I pre-ordered I could get Ocarina of Time: Master's Quest.