Zelda's gameplay didn't change when it went to 3d. The graphics did and thus the level of control over the character became more complicated and depthened just as for example the new Castlevania on PS2 though lacking most of the depth of 2d Castelvanias it depthens the combat. There is a middle ground that Konami must reach in this case.
With Zelda the series is traditionally played in three quarters view just as most landscapes are painted from a three quarters view with a high horizon which flatens things making them more graphic. The reason is because for most reasons this view is best, not only asthetically, but also in offering freedom in character control. With WW the camera system was up to the player thus the view was nolonger set behind the character giving only a low horizon line view or a close top down view offering little in seeing the surroundings. I believe Nintendo listened to complaints about camera view needing to be an option as many of us realized that most of the time three quarters vantage point offers alot more except in some cases when you can easily move the camera yourself. So you can choose a more 2d profile view that really shows how 2d vs 3d is not really a fight of whether it really is 2d or 3d, but rather whether the view is 2d or 3d.
As far as WW, Oot, and LttP being related in design I will say that the series has always been all over the map as far as how the games look. I felt that OoT wanted to be cel shaded like WW so that the character designs in the game (and the ones from the old games that didn't make it into OoT because they didn't fit at all with the asthetics) would fit the appearance of the game. Also cel shading's flatness is very true to how we see in 2d shades which is remenescent of old school 2d graphics like in LttP.
Mario 64 was a great game; amazing how people have selective hearing, but it didn't play like a 2d Mario because Nintendo was new the game of 3d. I believe now; just now, that Nintendo is seeing how supperior 2d is to 3d in offering accessable views rather than gameplay that must be riged up to get the player to roam fully in 3d rather than taking a path. Once again let me say that Zelda was always more lending to a 3d engine with a view that was although 2d, it was also able to offer a 3d illusionistic experience. I don't believe N64 had the power to do a 3d Zelda.
Before I go I want to say, that stuff about Nintendo not wanting to do a realistic Zelda because it would have glitches is ridiculous. Just look at Metroid, which I also hope will become cel shaded (similar to Ico). What's going on is Nintendo is being economical rather than ambitious these days.