"There are three major details in Wind Waker's story that just clashed huge with what I accepted as the existing Zelda storyline. First the villain returns... as Ganondorf? Up till now the assumption was that Ganondorf was his human form and he turned into Ganon which is the form he has remained in every since. But in Wind Waker he's back as a human and never turns into Ganon. That just seemed very out of place to me."
To me it seemed as if Ganon was just tossed into OoT. Sure, his name was Ganondorf, but it just seemed like sticking with the old games for the sake of it rather than continuing anything. As far as I'm concerned, Ganondorf is another villain and Ganon is simply a form he took.
"Next there's the freaking flood. How the hell does the entire world being flooded fit into the Zelda storyline? Somehow Hyrule exists after Wind Waker in a form very similar to how it looks in Ocarina of Time. I really hope they have a good explanation for this in the next game."
The reason for the flood is laid out clearly in Wind Waker. Also, you're assuming a timeline exists, when it really doesn't. A Link to the Past does not necessarily occur after all of these games. Even if Nintendo said that, they were BSing because they don't really have a timeline set up.
"And finally they set Wind Waker at 100 years later which makes no sense. That's too short of a time for the insanely huge differences between Hyrule and 'Floodville' to occur. Evolution in only 100 years? An entire legend lost in the annals of time being only 100 years old? Imagine how silly it would sound to talk about 1905 as some forgotten ancient era. That's pretty much what Wind Waker does."
Well, 100 years is a much longer time without photographs and videos and other forms of memory other than oral transaction and literature. Besides, think of this: what happened in the past century? Cars, airplanes, two world wars (and a multitude of smaller ones), radio, television, computers, the internet, all of that. Plenty can happen in one century; not even that much happens in Wind Waker, so it's totally reasonable.
It also clearly explains that the Ritos did not evolve, they were given their wings by Valoo.
EDIT: Bill explained my point regarding the time that passed. Thanks in return

I do see Wind Waker as ignoring the timeline, though. Which is fine with me, because I refuse to believe one exists anyway, and thus far all evidence seems to be in favor of me.
They are games, and the first ones are disconnected from the new 3D ones entirely. Too well.