Sorry to bump an old topic, but i just beat TP and here is my take on it.
About Ganondorf not recognizing the Master Sword, it's said that a Gerudo male is born every 1000 years. That male is probably Ganondorf, kind of like the hero of time reincarnation.
It was probably around 1000 years between OoT and WW if i remember correctly.
Ganondorf was born prior to the start of TP, TP happens and at the end of it when link stabs ganondorf with the sword he could easily be stunned. Maybe the Master Sword can remove the power of the Triforce from people.
Anyway, They could of easily shoved Ganondorf somewhere if he were still alive, maybe in the Twilight Realm, he stays there for a long time, Link dies of Old age. Maybe if that happens then the Master Sword would be powerless, Ganondorf then gets his Triforce of Power back. He breaks out of the Twilight Realm and floods Hyrule.
During that time he could of done research and found out about the Master Sword, then WW takes place.
Just a theory, which no doubt has alot of holes in it.
Please point them out.