I like Volvagia's story in the manga.
I think that, maybe dragons of his variety become more dangerous when they grow up - not only bigger and stronger, but baser in instinct... but I also think that Ganondorf put some kind of spell or possession on him, corrupting him beyond salavage. I tend to think that this is what happened to the Twili, too, in Twilight Princess - that they were once innocent people who were transformed and corruted and that any semblance of their old selves or souls they have left are trapped within the corrupted, obdient to Evil forms.
Maybe Ganondorf just got ahold of Volvagia to "awaken" or train him. Perhaps it's kind of like taking a small puppy - cute, innocent, eager to please - and kicking it and beating it, and starving it, training it to hurt people/other dogs/small animals by rewarding it with food only when it does so. What you are left with is a vicious, dangerous dog that's very different from the small puppy you used to know. There's a reason why pounds and humane societies put down a lot of pit bulls - and it's not because they are an "evil breed" - I grew up with one that was raised with kindness and treated right, and so, became a good pet dog. I can easily imagine dragons being the same way - naturally very strong creatures who will be as "good" or "evil" to people as a master would train them to be. Sadly, Volvagia lost Link as a master sometime when the kid went into his seven-year sleep, and quite possibly was taken by Ganondorf and/or his minions.