As long as I'm thinking along these lines, I'd better mention the worst flaw of Confucian political thinking in my eyes, which almost all authoritarian systems share (democracy can be equally bad, but usually it's more reliable). I'm talking about succession to the various high offices, and to the ruler's title itself.
A technocratic hierarchy, with exams, bureaucratic tradition and all that, can fill the more technical posts well, but the most important offices, like those of ministers and the ruler, are political in nature, meaning that even an efficient specialist holding them can still be seen as "evil" if he implements disliked policies. The doctrine of the "Mandate of Heaven" allows displacing a corrupt or incompetent official, but if he's doing something not forbidden by it, yet widely hated, like sending conscripts to die in a far-off war instead of paying a tithe, it necessitates either rule through coercion or an "unlawful" uprising, and the doctrine is discredited. Look at modern China: people might be hesitant e.g. to speak out against censorship, but they are understanding that the government actively disregards their wishes, and they'll disrespect it in turn, so preaching "harmony" to them will fall on deaf ears and, in the absense of other legitimizing mechanisms, stability might decline.
Therefore, we'd better take into account how vulnerable the doctrine of obeying a "virtuous" or "proper" authority can be.