Well Ganon appeared in previous games BEFORE Ganondorf was born. You can't transform into someone else if you don't exist yet. I think what happened is this:
In the first LOZ, Ganon was defeated by Link with the "Magical Sword". The Magical Sword was not the Master Sword. Ganon was not killed, he just disappeared. Then, in AOL, he returned and once again tried to rule the world. Another Link rose and triumphed over him, but without the Master Sword. In LTTP, he broke free once again. He found Ganondorf and put him as his main man in his army. Like the Queen, only a man. Then, yet another Link rose, but too early. He found the Master Sword, but was too young to be the "Hero of Time", so his spirit had to be kept in the Temple of Light for 7 years. Once he rose, he defeated Ganon, and returned to his own time period. However, since this was before Ganon was defeated, he sent the Skull Kid to steal the Majora's Mask. He distracted Link long enough to nearly destroy Hyrule. Anyway, to find out more you'll have to play WW. I'm not spoiling it for anyone.
Everybody has the right to stupidity, but you''re abusing the privilage.