He also doesn't have the ToP when he gets stabbed in TP.......I still fail to see how it's any different. Also, the King of red Lions made a wish before Ganondorf did. Wouldn't the triforce break apart again after the wish was made? And if it does break apart again then wouldn't Ganondorf have the ToP back? With that in mind, maybe he did have the ToP when he turned to stone. If he didn't, why would some normal mortal turn to stone instead of just die when getting stabbed in the head?
Your still not getting what I am saying. ALttP's backstory has yet to be played through or shown to anyone, other in that game. The manual talks about Ganondorf as a man gaining access to the Sacred Realm and obtaining the Triforce. According to my timeline, this event should come sometime after OoT (since it can't be OoT) and sometime before ALttP. Seeing as how TP takes place between those games, and does not show this event, it gives a place open for Ganondorf to still be alive somehow.
The Triforce obviously leaves Ganondorf, or loses its power it is giving him at least at the end of TP. In WW, it floats off. If it went back into Link, Ganondorf, and Zelda, it would have shown that, but it didn't. It obviously went elsewhere to be discovered again at a later time.
If the ALttP backstory was something other than what it is, then I could see Ganondorf completely dying at the end of TP. But they still have that one story left to tell. According to my timeline, there is no backstory telling events that should come after WW, unless you wanted to put ALttP on that side of the timeline or something. Either way, Ganondorf should have one game left.