Tokugawa Ieyasu's power base in Japan back in the 1600s was in the Kanto region, which was given to him by Hideyoshi after the Hojo clan was defeated. As such, the Shogunate's residence was in Edo, where his personal demesne, if you will, along with his most loyal retainers and armies. So while the Emperor stayed in Kyoto, the center of Japan shifted to Edo. By the time of the Meiji Restoration, Japanese governmental institutions were so entrenched in Edo that it was convenient for the Meiji Emperor to just move into the former Shogun's castle, which became the Imperial Palace.