As others have stated, the Byzantine Empire was a remarkably durable state. Certainly there were ways in which specific episodes of instability or specific civil wars could have been avoided, but given the limited resources of a pre-modern state I consider them to have done remarkably well.
As for "assimilation," I don't consider the Byzantines to have "failed" in any remarkable respect. Ethnicity is not written on the hearts of men - it is a created thing. One must be taught to be Bulgarian, Greek, or "Roman." Being a pre-modern state, the Byzantine Empire did not have the capacity to teach a culture wholly out of existence as is now possible with modern bureaucracy, education, and media. No doubt things would have been easier if Basil II could have marched his Imperial Scholastic Corps into the public schools of 11th century Bulgaria to teach everyone how to be a good Roman and make sure nobody spoke a word of Bulgarian during school hours before sending them home to watch "The Adventures of Young Constantine" on the TV (broadcast entirely in Greek). It seems to me that for a pre-modern society they did a very good job of using ethnic minorities in service to the state and investing them in the imperial project - just look at the outsize role the Armenians played in the empire's long history.
In any case, focusing on the "assimilation failure" angle is too blinkered and arguably puts too much importance on proto-nationalism. The Second Bulgarian Empire, for instance, began as a tax revolt, was started by men who had been refused the imperial grants they wanted, and would have been stillborn had it not been for the massive intervention of foreign military forces. Why choose "failure to assimilate Bulgarians/Vlachs" as the cause of that rather than, say, "failure to secure the borders against the Cumans" or "failure to maintain a manageable tax burden on the people" or "failure to properly satisfy applicants for imperial grants?"