The doctrine I choose to hold about this question, "Why did God had to wait 4000 years, from Adam to the book of Malachi, for Jesus to come in the flesh?" is this:
It was a man—a physical human being—who had been given authority on the earth by God. When man allowed himself to be deceived and when he yielded his power to Satan, he became, in a sense, joint-heirs with the devil. Satan has to work through a human being. Man, through his physical body, gave Satan authority on this earth.
Therefore, it was necessary for a man with a physical body to take back that authority. God had to become man, to give Him the authority to execute judgment on the earth: “And hath given him authority to execute judgment also, because he is the Son of man” (John 5:27). God cannot break or change His word, so He was restricted to act within the word He had already spoken.
But why did it take 4,000 years? Here is the logic: When God created the first man, He said, “Let us make man in our image” (Gen. 1:26). He literally spoke Adam’s body into existence. At that time, He had the legal right to do that because He had not yet given authority over this earth to man.
However, once He had given that authority to man, He could not leave him out of the equation. The last Adam, Jesus, would still have to be spoken into existence by God, but He would have to speak through man. God was no longer in direct control, and a man would have to become the voice of His words. Psalm 115:16 explains—
The heaven, even the heavens, are the Lord’s: but the earth hath he given to the children of men.
That is a strong statement. In other words, everything outside of the earth belongs to God, but the earth He gave to the children of man. God literally placed restrictions on Himself through His own words. He had to work through people, and there were very few people sensitive enough to hear Him in their hearts and then prophesy what they heard.
God had to create the new Adam through words spoken by someone with a physical body. Galatians 4:4 says, “But when the fulness of the time was come, God sent forth his Son.” If you study that out, it means at the appropriate moment. Until then, all the prophetic utterances hadn’t been spoken. Jesus could not come onto the scene until everything that had to be said was said.