Board Thread:Questions and Answers/@comment-2211792-20130314065111/@comment-893506-20130314075951

Yamamoto was the strongest Shinigami born, and Ryujin Jakka is the most powerful Zanpakuto in existence. Aizen knew that in order to achieve his goals, he would need to cripple Yamamoto's fighting ability, and Wonderweiss sealing Ryujin Jakka's flames would do just that.

Additionally, even though Aizen had the Hogyoku implanted in his body, it wouldn't simply just increase all of his power at once. Look how long it took to change to each of Aizen's forms. It didn't start changing him until after Isshin worn him down and pushed him to the limits of his power as a Shinigami.