You could dive into the complex relationship between Shogun and Emperor and analyse the critical differences between the two offices, such as the role of the Emperor being largely ceremonial and religious (not to be discounted however - this role held huge cultural significance) or the Shogun being essentially the supreme military general as appointed by the Imperial Court. The Shogun's power came not only from his (and his clan's) military strength, but also from the legitimisation of his role by simple law (via proxy of the Imperial Court and the Emperor) - indeed, the original and simplistic idea of a supreme military general came forth out of a direct need for a centralisation of the scattered military powers of different families. At the same time, samurai as a class became more defined, however the extents to which they were able to exert their power were still very much limited by the will of the Imperial State. Prior to the establishment of a formal shogunate (the end of the Heian period), due largely to the Buddhist/Chinese influences that reached Japan, the Emperor and his Court were considered (and still are) the divine authority and representative of the heavens, and was the supreme military commander.

However, this changed in the transition to the Kamakura shogunate under the Minamoto family - the Emperor was relegated to a religious figure and ceremonial role, despite them ironically being what legitimised the Shogun's power. During this entire period (and subsequent eras), emperors could and were forced to abdicate by the Shogun, however again there was no formal 'usurping'. As you can imagine, this was a large issue for the Emperor, and so in 1221 the first Emperor during the Kamakura shogunate, Go-Toba, declared open rebellion against the shogunate in a bid to reclaim his authority and power (after being forced to abdicate and having various sons/grandsons used as puppets by the Shogun). He lost due to a number of factors, including direct intervention by the Hojo clan who began to directly influence the regents of the shogunate - complicated politics ensues, another emperor further down the period makes plans to overthrow the Kamakura shogunate. The Imperial Court came back into power, briefly, before being disposed of by the Ashikaga shogunate.

Nevertheless, the Emperor's role was still one of cultural importance to the people, even if they were controlled by the Shogun. It's hard to emphasise exactly how much cultural significance the Imperial Court had - it was enormous, as it was the solidarity of many years of religious and cultural ideologies that allowed the Emperor to be a figure of divine authority. So, to more directly answer your question - there was no reason to formally usurp the emperor and upturn the entire idea of cultural values. Whilst you see a more concrete fusing of the Court and the Shogun during the Tokugawa shogunate/Edo period, the Emperor was still an individual separate entity to the Shogun, and retained his religious and cultural value. The throne was not less desirable nor less feasible, however it nevertheless still cemented the authority of the Shogun, and thus no Shogun would formally usurp the Emperor - there was no need to risk widespread rebellion, when puppet Emperors were able to be manipulated just as easily.