Wind Waker is literally the tale of the spirit of the hero no longer being available and a new person stepping up to the plate to being the cycle once again.
Amusingly, the only reason this happened was due to Link going to the past in OoT. If he didn't, there wouldn't be a flood, the hero would appear as usual, and so on.
It's worth noting that the 'hero' doesn't feel like much of one, mentioning how he lingers around in the after-life because the lack of recognition as a hero (despite saving termina). His actions are largely forgotten or ignored, since all he 'did' in the past is warn of ganon. And in this branch, the sages get much of the praise, not Link.