I remember loving OoT as a kid (I was a huge Nintendo fan and therefore HAD to play it). I also blindly defended the series based on the two games I had actually played at the time (OoT and aLttP) As time went on I played MM, Legend Of Zelda, Zelda II, Link's awakening, the oracle duo, Minish cap, wind Waker, four swords adventures and Twilight Princess. It was somewhere around Wind Waker when i realised that OoT was a much more inferior entry in the series and that the only reason I, and in my opinion, most fans idolised it was because it was the first 3D Zelda and because it was nostalgic.
In my opinion the series isn't that great storywise (in fact I find it average at best) and up until wind waker a lot of the characters were lacking in, well, character. One thing that always stuck out was the music, it was superb.
I feel the best entry in the series is Wind Waker, it was (and is still) beautiful. The music, characters, the cartoony style, the scale, the visuals were epic. And even the story strayed from Nintendo's classic "save da princess" plot. I also feel MM is probably the most under rated Zelda game, it was fantastic, the moon, the 3 days etc, it was really clever.