There's no over-all time line as Nintendo didn't persue one and only recently (~past couple of years) have tried to rationalise it all. I think inreality each game was basically an update of the previous as technology got better. Certainly, Link to the Past was essentially replayed in Ocarina of Time .
IIRC WindWaker, with it's great flood theme, was to be treated as a tangent and persued to it's own conclusion.
Shame. The game wasn't awesome but I thought the mechanic interesting. Plus, the brief visit to Hyrule looked great with cell-shading IMHO.
oh and, as for bosses, Armor Knights FTW! Or Fake-Gannon in OofT.