there are a few things i think i need to say here...
the wind waker was not flawed and oot and mm were nowhere near perfection.
evolution, friends...evolution is what promoted everyone's love of oot. it had a new style for the zelda fans, a 3-d style...this alone caused an outcry of yay's and hoowa's...
the game itself isn't that amazing, it only follows a basic guide for great games (as all zelda games do)...amazing story+great gameplay=a great game...
no one had seen a three-dimensional link before; add this to the epicness of the game and, blamo, a hit!
mm was great (not perfect) but very underappreciated...it was much deeper than oot, providing more character development and emotion. unfortunately, as was said, it had a weak outside gameplay...the dungeons were stellar and way above par, but everything else, characters and story aside, was rather weak and somewhat short...
flaws in ww?
barely...the only ones i could think of were a long and sometimes tedious travel system and an alltogether short experience...the arguement about the game being "too easy" doesn't fly to well...
maybe for an experienced fan it was easy, but for any old joe wanting to get into the series, this was a great way to start, so enough of that...
i find it nearly impossible to compare zelda games, simply because they are all great games...they each add new and improved elements as well as their own specific and recognizeable style (though quite similar, at times)
so try not to go blowing off ww because it wasn't "as good" as oot, or saying mm had a weak gameplay in comparison to ww, or any of that...(definately don't talk trash about future games either, cause they don't exist) becuase you can't.
like i once said, comparing one zelda game to another is like comparing one apple to another slightly less red apple...they are both apples, and they are both awesome, so enjoy them all!

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...never knows best.