Confucianism has several issues, including but not limited to:
1.) It's indictment against 'superstition' has been interpreted as supporting atheism (as far back as the Three Kingdoms period one warlord killed and tortured Daoists because of it).
2.) Confucius never gave any space to rebel. Ever. Period. Full stop. Rebels are always wrong, no matter how bad the leader is. Mencius does give framework to rebel, but they're promoting Confucius not Mencius aren't they?
3.) Similarly, parents are to be obeyed. Always. Forever. Full stop. It doesn't matter if they mistreat you or even are going to kill you, you are supposed to obey and accept it.
4.) Extreme politeness and etiquette to the point of ridiculousness, with no room to question the rituals or reasons for the etiquette.
5.) Misogyny, women are inferior. (For example, the five bonds in common order of importance are: Ruler to Ruled, Father to Son, Husband to Wife, Elder Brother to Younger Brother, Friend to Friend. Note both that a woman is put in the inferior position and is considered less important than Father/Son and Ruler/Ruled relationships). Further, they are supposed to be at home, caring for the home, have less Human rights, virtue, and so on. Polygamy is also permitted, if you consider that misogynistic (as some do).
6.) Veneration of ancestors and practical worship of the past (the whole gotterdammerung sort of thinking) can definitely lead to backwards looking views. The old ways are often presumed to be best.
7.) Social mobility except through pre-ascribed routes is considered bad. Peasant farmers shouldn't want to stop being peasant farmers. The fulfillment of their life, as Oniya mentioned, would merely be to be the best peasant farmer they can. Now, theoretically there is room for meritocracy, but what they are looking for are gentlemen such as described below:
8.) Gentlemen at the center of everything, which suffers from a lot of the same elitism of Plato and the like. The Gentleman is the most important member of society, the most learned, wise, educated, and so on, and comes from the right social class. He is society's moral and social guide. They are supposed to be a scholar-saint-sage, and this suffers from all the problems of an aretaic morality.
9.) Down-Up responsibility means that people have obligations to their superiors, often in excess of what rulers have to their people in turn. Often times people only have obligations to their superiors with little in return necessarily (on the presumption the superior will be good and therefore return their loyalty regardless).
10.) Legitimacy comes from a version of the Divine Right to Rule (the Mandate of Heaven), the people and their consent have nothing to do with it.
11.) Denunciation of businessmen (the lowest 'acceptable' class in China were merchants) and the veneration of farming. Also, support for class division with nobles at the top.
12.) It endorses the old authoritarian view of rule (the state/ruler's power is unlimited except as how it chooses to limit it) rather than the modern liberal view (by which I mean 'a modern view that came from 19th century liberals') that a government only has power in the areas it is defined to have powers.
Keep in mind that the demands of the early 20th centuries anti-Confucianists were as follows (in other words, Confucianism was at least used to support the opposite of all these things):
+Acceptance of vernacular language
+Individualism rather than family structures reigning supreme
+Egalitarianism (including women)
+Renunciation that Chinese values are and China is superior to every nation everywhere
+Allowing Critical examination of Confucian texts
+An end to the obsession with the past
+Investments in, and acknowledgment of, Western science
Now, Confucius is not all bad. But like Plato you have to realize that his view is not perfect and does not fit perfectly into modern society. It's been used to justify some ugly things, like every ideology has as well. In any case, I have to say that it appears to me the Chinese government specifically picked a philosopher who stressed obedience because, well, they're a government. And I expect them to spin it like no tomorrow.