First off: Ganondorf's blood was changed to green because parents complained. The green blood was a way of censorship.
Ganondorf's green skin is likely just a skin color of powerful, magic wielding gerudo. His surrogate mothers, Twinrova, also has green skin if you notice. I'm fairly certain the green skin is something of Gerudo attributes. They wanted to make his skin dark, to represent he spends much of his time in the desert sun, and yet they didn't want to make him black... as that would be rather racist and Nintendo had an issue with that in the past. (The Pokemon Jynx)
Gamewise though, I'm sure the green skin is the fact that his body has been corrupted by dark magic, much like Twinrova. I think Twinrova may actually be Ganondorf's mother... and former matriarch of the Gerudo people. Kaume and Kotake are possibly the fate of the woman after birthing the dark king... She split into two parts. Only able to combine in dire need. The fact that she dies after taking this form... despite living hundreds of years... makes sense. But this is all just speculation.
I also believe Ganon pre-existed the birth of ganondorf, and saught human form. The birthing process of the Gerudo is still yet unknown however... maybe they aren't born in the traditional sense at all. Something to ponder I suppose.
But surrogate
