Ocarina of Time actually has my least favorite overworld out of the five Zelda games I've played, and I really don't see why people are praising its overworld in comparison to the ones in WW and TP. In OoT you just have a big circle connecting everything and that's it. In MM it's the same thing except that Clock Town is at the center of the overworld. In WW and TP, however, the overworld simply contains loads of cool locations, instead of merely being a "hub" of sorts.
Also for me Twilight Princess and Wind Waker have a lot of awesome scenic views in their overworlds which the two N64 games can't hope to match. Also, in Twilight Princess the "huge, empty" overworld is worth it for being able to let out the speed while on horseback, something I really can't do in either of the N64 games.
My Ocarina of Time "hate" has been well-documented by now, but for me it's far more of a victim to its own era and the fact that later Zeldas, especially Majora's Mask and even more especially Twilight Princess, dilute its appeal. This is not to say I can't appreciate anything from the N64: for instance I do not feel the same way about Super Mario 64 because that game feels more like a "completely different animal" within its series, plus the game has more of an SNES-feel to me than an N64-feel.
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