Twilight Princess takes place "decades" after OOT, according to Nintendo Power.

Phantom Hourglass is a direct sequel to Wind Waker (same Link) according to... damn, I forgot the source. Shoot.

The Link in Wind Waker isn't a decendant of OOT Link. I'm not sure where you got that. It never said anything like that in Wind Waker.

Also, I'm sure the general belief is that not all of the Zeldas are connected.