I confess that I thought Wind Waker was a good game, but hardly the best in the series.
To me, the first hours of the game were the best. Meeting Tetra, the Red King, trying to defeat the bird that kidnapped the girls, finding out Tetra's secret, going to the flooded Hyrule frozen in time, meeting the King of Hyrule, going to Dragoon Roost Island for the first time, these were perhaps the best moments in the entire game.
Afterwards, the game got boring and tedious, and showed the creators were pressed for time and rushed through the final arc. I mean, you only go to two of the seven dungeons based on the sages, the triforce collecting got VERY tedious and it just wasn't that fun.
Even the final battle with Ganondorf seemed rushed. I was expecting a multiple battle finale where it would take a lot of hits in order for Ganondorf to be defeated. Even if the final attack was cool as all hell I felt disappointed.
As easy as the Ganondorf battle was in Twilight Princess it delivered in terms of epic-ness and drama.
So yeah, WW was a good game but to me it could have been more.