I would have to say that I somewhat agree. The writters are more likely to make certain theories a reality when writing a game's story. This is kind of a bad example, but it's more likely that the writters will introduce a single timeline than for them to say that TWW was Tingle's bad dream. When making a game about the beginning of the flood (which I guess could be TP), they are more likely to say that Ganon is directly resposible than to say that Tingle helped Ganon out and made the Alliance of Evil.
Anyway, I have other reasons than just the chance for believing that TWW is a "what if" scenario. Think about it. We see Ganon, the Master Sword, the Triforce, and Hyrule itself buried under the Great Sea. Basically, every element important to a (major) Zelda game was killed off. To me, that makes a statement. For example, I wouldn't have expected Shakespeare to write "Hamlet Part II" because (OMFG SHAKESPEARE "SPOILERS"!!!!!!) everyone in Hamlet is killed off. He could have wrote a Hamlet prequel because every person and element that it took to write a play in the style of "Hamlet" would have still been alive at that point in the "Hamlet" universe.
I guess what I'm trying to say is that if the Zelda series continues to deal with the TWW story line, they will either have to make prequels, like (possibly) TP, pseudo-sequels, like PH, or just say that TWW was a "what if" scenario, and just deal with the games made before TWW.
Again though, the only element that can't easily be explained in the Master Sword. Think about it. The reemergence of Hyrule is heavily hinted at in the game.
DEKU TREE, TALKING TO HIM AFTER CEREMONY:
Every year after the Koroks perform this
ceremony, they fly off to the distant
islands on the sea and plant my seeds
in the hopes that new forests will grow.
Forests hold great power--they can change
one tiny island into a much larger island.
Soon, a day will come when all the islands
are one, connected by earth and grove.
And the people who live on that great
island will be able to join hands and,
together, create a better world.
Such is my dream.
...But the one you are chasing is trying
to prevent that dream from ever coming
to pass.
GANONDORF:
What did the King of Hyrule say?
...That the gods sealed Hyrule away?
And they left behind people who would
one day awaken Hyrule?!
KING:
I have scattered the seeds of the future...
Now Ganon's quote is rather dubious because he seems to be saying that they'd one day awaken the real Hyrule and the game never states this elsewhere, but the King does make it clear that Hyrule would remain below as long as Ganondorf was never "revived" (revived meaning brought to the full luster of his power since Ganon was sealed beneath the waves with Hyrule). If he meant it in the context of unsealing Hyrule than that would make no sense since to unseal Hyrule would mean to unseal Ganon, and he was meant to be sealed for all time.
And of course the King's comments could be interpreted different ways (seeds could mean Link and Zelda since he says this in the context of finding a different land), but the Deku Tree's words are clear, and the fact that they both used the words "seeds" makes me think that they're both refering to the same thing.
The point is, Nintendo clearly inserted a number of references to make sure that Hyrule could be rebuilt. Obviously they didn't completely neglect future games in the series and mean WW as a stand alone thing in that respect.
We never really see what happens to the Triforce. The most common theory is that it flies back to the Sacred Realm. The only other game the Triforce is collected in its entirety and wished upon was at the end of LTTP, and it appeared the Triforce went with Link to Hyrule (although I don't believe it ever shows this). However, there are a number of variables to consider. With the King as the sole owner of the Triforce, perhaps he never intended for it to stay with him. Or if it did, he was killed as the sea swallowed Hyrule, so without an actual resting place there really is no canon for what could potentially happen to it.
Ganon is both easy and hard to explain. Easy because even if he's killed he can be resurrected. Ganon is never a problem to deal with, although his placement is somewhat tricky. If WW happens before LTTP than Ganon would have to end up resealed in the Sacred Realm. The problem is...what happened to Ganondorf? Was he resealed in the Sacred Realm? Did he die? Was he simply sealed in a chunk of stone? What you're saying with a what if scenario is that it simply destroys everything we've known about the series and starts over, but Ganon can be revived, even without the Triforce, so that doesn't really solve anything. It's not like you can say he's permenantly destroyed, that's the end of him, we don't have to deal with him in the timeline again. Wind Waker is interesting because it's the only game where he is defeated as Ganondorf. This brings up even more questions. Does he retain all of his powers even as Ganondorf without the Triforce? Are Ganon and Ganondorf in essence interchangeable? See these are questions that have to be answered no matter what you believe because they heavily effect the outcome of the timeline, and right now there are no answers.
The Master Sword is just impossible to expain right now without more hints at it. As an aside, I find it funny that in Oracles you can get a broken sword from a Zora that turns into the Master Sword if you already have the Noble Sword. I'm not saying there's any connection at all. I don't believe crazy theories like that. But it's certainly coincidental. I don't think there's any way that Oracles happens before LTTP though.
The point is, there are obvious connections in WW that link to other games, most importantly OOT, so it has its place within the timeline. It's heavily infered that a new Hyrule comes to be, so we simply need a future game to explain what happens to the Master Sword and Ganon.
As for OOT, I formed a theory awhile ago that said the seal was retroactive. In other words when Link went back in time the seal itself was in place so Ganon was trapped there anyway. It's similar to what other people are saying without the need for an intemporal Sacred Realm. Of course this isn't very well thought out since there's no real explanation as how this could happen and it doesn't explain the emergence of the Seven Sages because they obviously play a future role in the series. And I haven't even thought about how it impacts the meeting between Link and Zelda at the end. I'll have to go back to the drawing board and flesh this out or make some changes. In fact I haven't really thought about the ending to OOT at all in the past eight years. It's just not that important to me. I even doubt whether Nintendo had a real meaning or real thought as to how it effected the rest of the series. Hopefully TP goes far to clean this up.