The only explanation as to why the ToP wasn't enough for him to keep his physical form is that the wound inflicted on him by the sages made him susceptible to the effects of Twilight.
@Mr. Mander: I have a problem with your theory. Ganondorf wouldn't need the pyramid. He could just sit back in Twilight covered Faron or another province and wait for the light to be restored, by your logic. It's my belief, although I think Ganondorf needs a more prolonged and gradual exposure to the Light than you imply.
I just don't think Nintendo thought it through properly... I know that's like the most cheating sentence a theorist can resort to but...
*What actually happened*What if Vaati had been sealed, not destroyed, in tMC*
*As blue, plus what if Midna had not destroyed the Mirror of Twilight*What if Link had failed in OoT*
*What if Link had failed in OoX and Ganon changed his name to Gannon*
^It isnt a positive thought, but I agree with you River Zora. We have a host of suspect questions - actually, we have little explination for a plethora of behavior from many characters.
Infact, Looking closely at Twilight Princess, we truly are seeing a rehash of the Triforce saga from Ocarina Of Time - with a twist. The Fused Shadows make an entrance, yet the source of the plot remains the same. Behind Zelda blessing Midna, and Ganondorf 'housing his power' in Zant, we have a badly diverted form of the latter plot from Ocarina - the Triforce holders.