Just a thought, but what if Ganon's intelligence depends on the body used to resurrect him? Maybe his mind can only reside inside an inheritor of a part of the Triforce. This is why Twinrova wanted to use Zelda's body for the resurrection. Also his followers are trying to use Link's blood in AoL...
He seems to have returned to human form twice in the Adult timeline, so I wouldn't say the pig form itself is evidence of him losing his identity as Ganondorf. But in everything after A link to the Past, Ganon seems to be pretty much inseparable from Demise since he keeps coming back after being...