I was reading about Ismaili theology, and it seemed to be incredibly different from both Twelver Shia and Sunni Islam. How did these changes come about?
Well, there are different branches of Ismaili Islam, some defunct, some extant. As with all Shia, they differ from Sunnis in their adherance to the Imamate, the spiritual leader of specific descendants of Ali. In the case of the twelvers, there were twelve of these Imams. Ismailis are so named because their claim that the seventh Imam after Jafar as-Sadiq was Ismail ibn Jafar, whereas the twelvers hold that it was his younger brother Musa ibn Jafar.
From this point of departure there are radically different groups of Ismailis. These include, in no particular order, and some of which descend from one another, the Fatimid Caliphate, the Qarmatians, the Assassins, the Bohra and the followers of the Aga Khan.
Of these, the followers of the Aga Khan are probably the most prominent extant group. Formally they make up branch of the Nizari Ismaili Shia. Their leader, Aga Khan IV, is the 49th Imam by their reckoning.
Like the other such groups, their distinctions are in large part due to their having the leadership of a much lengthier Imamate. As they still have a living Imam, they are ultimately less beholden to conceptions about emulating the past in comparison with schisms or sects that had to establish dogmas surrounding the teachings of previous Imams when their respective Imamates ended, or with Sunnis who are so named for their emphasis on the prophetic Sunna, the "path" or model of the prophet as recorded, reconstructed and interpreted through centuries of religious scholarship and consequent religious legal jurisprudence (fiqh) derived from these sources of the Sharia (the Quran, the Hadith, Consensus, Analogical Reasoning, and, previously, independent reasoning) by the Sunni Ulema, the religious scholarly class.