The Ottoman millet system sounded like it would have worked in theory. The millet system sometimes worked. But the Ottoman millet did not always work in practice. The Ottoman Empire often tended to be repressive against its subjects in the empire, some areas more than others.
Self-government is certainly a good way of preserving peace in a region. Self-government and autonomy certainly especially makes sense in Syria with the religious and ethnic diversity. I feel this is where we find the answer to what caused the current crisis.
The Assad Regime and the Syrian Ba’athist Party has little tolerance for religious and ethnic diversity. They push for a certain political ideology over other political ideals.