The issue wasn't that China was not centralized. It was that China had been top dog for centuries and the Chinese were supremely confidant that everyone else was inferior. Very few felt they needed to change until it was demostrated again and again that the Europeans had better militaries and were an actual threat.
Machiavelli wrote in the Prince:
"It must be considered that there is nothing more difficult to carry out, nor more doubtful of success, nor more dangerous to handle, than to initiate a new order of things. For the reformer has enemies in all those who profit by the old order, and only lukewarm defenders in all those who would profit by the new order, this lukewarmness arising partly from fear of their adversaries, who have the laws in their favour; and partly from the incredulity of mankind, who do not truly believe in anything new until they have had the actual experience of it.''
In other words, anyone who attempts to change China is going to run into all sorts of trouble. This isn't so much to do with any aspect of Chinese culture, but basic human nature. It is very rare in any country's history that someone can radically reform their society. Instead, reform comes only after repeated defeats that discredits the old regime, or comes only after a long period when the culture "digests" the once radical notions so that it becomes part of the culture.
The fact is that lots of people benefited from the way China did things. None of them are simply going to agree to changes that threaten that directly or indirectly. Strange and novel ideas naturally repel people as they seem to threaten the social order, and thus stability. When threatened by defeat, the first response of most societies is to think, "We were successful before, so why not now? It must be because we've deviated from the way our people used to do things. We must go back to the way our culture used to be and get rid of all these innovations that have crept in since then."
People tend to overstate the ability of despots to make changes in their society. Peter the Great did it, but that was an outlier. He encountered significant opposition, but succeeded because the earlier Russian Tsars had effectively destroyed any countervailing power. China, though, has lots of ways for people to thwart any reformer, including an emperor. There is the entire Mandarin bureaucracy based on the study of classic Chinese texts. The eunuchs of the Forbidden City. The commanders of the banner armies. All of them can sabotage reforms in many ways because the emperor simply can't know everything they are doing. Orders can be issued and simply ignored, or implemented in selective ways, or implemented in ways that discredit the ideas behind it. And it may not take much of such things for some kind of palace coup, which is very common in Chinese history, to remove the emperor and put someone else from the imperial family that is more amenable. Unless there is a broad based reform coaltion, any individual's reforms will likely be thwarted. And the earlier the time, the less likely such a broad coalition would exist.
As someone previously mentioned, the Manchu were not ethnic Han. They were outside invaders, and their only legitimacy was how much they followed Chinese ways. Too much innovation could cause them to be viewed as the troublemakers by the native Chinese.
So there are lots of obstacles.