Bottleneck

Once you realize there are three stages to materialize a government policy, the problem of the Ming government - as pointed out by Huang Zongxi (黃宗羲) - becomes crystal clear:

In short, without a prime minister, government policies were proposed and executed by government officials, but endorsed by the king (or eunuch by proxy), who would see things differently and became the bottleneck of pushing forward any important policy. Moreover, the system inevitably led to a conflict between government officials and the king (or, actually, eunuch).

For comparison, Han, Tang, and essentially Sung empires used the Three Department System (三省制): Principal Secretaries (中書省) made policy proposals, Under-Secretaries (門下省) endorsed and countersigned the proposals, and the administrative departments (尚書省) carried them out. (The English translations of the three departments are my own invention. My apology if they do not sound appropriate.) The three of them were independent but they came from the same group of people, and it was common to see officials promoted from one department to another - so that coordination was not a problem.

PS. In early Ming period, the king's decision relied heavily on his political advisers, with a poetic official title Principal Scholar of the Wenyuan Chamber (文淵閣大學士), so that the government could have an efficient running. I shall not bore you with the details further.