The thorn for the flesh was needed when Paul came down from paradise, so it was not that the flesh had got any better. The thorn was something to hinder sin, something that made him outwardly contemptible in his ministry. Every one would probably have a different thorn, according to his need. There is no change in the flesh, but the power of the Spirit of God is such that the flesh is kept down. "Always bearing about in the body the dying of the Lord Jesus" would not be necessary if the flesh were any better. It is not that there is any uncertainty as to salvation or acceptance, but that we should so walk through the wilderness that the flesh should be shut up, as it were.
God looks at us as dead with Christ, and we are called on to reckon ourselves dead. I have a title to do it because Christ has died, and I am crucified with Him. It is not only that we are born of God, but we have died with Christ.
In Col. 3 you find God seeing us dead. In Rom. 6 I reckon myself dead. In 2 Cor. 4 it is "always bearing about in the body the dying of the Lord Jesus, that the life also of Jesus might be made manifest in our body." This is going very far indeed. Death to Paul was so realized that the life of Christ only worked in him.