I'd like to think part of the reason it was so easy to control Kyurem was because it was devoid of anything, and was essentially reflecting the heart of its owner. The games at least suggest that the bond between humans and Pokemon can overcome the Pokeball's effects.
Personally, I prefer the idea that Ghetsis sealed his fate when he absorbed Reshiram/Zekrom. By having Kyurem's truth/ideals restored, Ghetsis' hold over it weakened and Zekrom was able to fight Kyurem from the inside. It could be a nice way of explaining why its level 55 then jumps 15 levels in its next appearance.
Personally, I prefer the idea that Ghetsis sealed his fate when he absorbed Reshiram/Zekrom. By having Kyurem's truth/ideals restored, Ghetsis' hold over it weakened and Zekrom was able to fight Kyurem from the inside. It could be a nice way of explaining why its level 55 then jumps 15 levels in its next appearance.