The endemic issues were many: the transformation of Anatolia into more feudal structures, the loss of defense of depth fostered by the Theme system, and the widening rift between the civilian bureaucracy in Constantinople and the land-holding military elites, an economic downward spiral, and as a consequence, a further degeneration of the military.
A couple of these issues I can agree with, but I think others are a bit dubious.
The
Themata were certainly moribund by the later eleventh century, but they had been slowly fading out of the picture from the 750s onward as the Empire returned to a system of paying professional armies in the form of the
Tagmata and foreign contingents. Seen from the perspective of the time, there was little reason to change this: the professional armies could and did defeat Turkish incursions, and the Seljuks themselves were no more scary than the Fatimids or Buyids.
The rift between Constantinople and the East I think is certainly an issue, but there's no real reason why it shouldn't be possible to close it. The rift had its origins in the tenth century, as the (Constantinople based) Macedonian Emperors struggled to contain the ambitions of their (largely Cappadocian based) warrior aristocracy. It was carried on into the eleventh century because the Emperors of that period explicitly tried to model their system of governance on that of Basil II- again, not unreasonable seen from the contemporary perspective. The breach could have been healed fairly easily if a Cappadocian took power and brought the interests of court and
Dynatoi together again, as happened (after a few false starts) IOTL with Aleksios I.
Economic downward spiral- yes, but that's not necessarily unsurmountable. What really began the process IOTL were the opening up of Byzantine markets to Italians, and there's no guarantee this'll happen ITTL. And of course even then, the process was not really apparent until the Fourth Crusade, which will certainly be butterflied in the absence of a major Turkish incursion into Asia Minor. The big problem is overcoming the distaste felt by Byzantine elites for any form of market capitalism that IOTL allowed the empire's trade and economic dominance to be "hollowed out" by the enterprising Italians.
As for feudalism, not sure I agree with that for this period. Byzantine power up until the Fourth Crusade was based on the holding of offices awarded by Constantinople, not independent landholding: this is true even for the Komnenoi. To finance those, a well organised tax-gathering system was needed, staffed by a literate and self-perpetuating bureaucracy. Neither of these facts about eleventh century Byzantium are conducive to the emergence of a feudal society.