It's important to understand the unique status of the Emperor in Japanese society — particularly during the various shogunates. The Emperor was held to be a quasi-divine figure; a direct descendant of the goddess Ameratsu.

In fact, it's only in 1946 (ie. during the dismantling of Imperial Japan after the Second World War) and on the insistence of General Douglas MacArthur, that the Emperor of Japan renounced his claim to divinity in the Humanity Declaration:

The ties between Us and Our people have always stood upon mutual trust and affection. They do not depend upon mere legends and myths. They are not predicated on the false conception that the Emperor is divine, and that the Japanese people are superior to other races and fated to rule the world.

So in the bakufu period we're talking about, the Emperor holds supreme sovereignty but is primarily a ceremonial figure; executive (temporal) power is wielded by the Shogun in the name of the Emperor. The Shogun's legitimacy (not his power, but his right to hold power) is derived from the Emperor.

So, the transition from one Shogun to another is a transference of temporal executive authority; but for a Shogun to declare himself Emperor would be a revolutionary (and I use that term very literally) alteration to the social/spiritual order and power structures of Japan.