Paul's used the word "exalted" here to show what the point of this messenger was, to keep him humble. Paul made it very clear that this "thorn in the flesh" came because of the abundance of revelations he had received. God is interested in keeping his pride in check because Paul would be used more than any other in relaying the revelations having to do with the new covenant to the church. God was not the author of this "thorn in the flesh but certainly allowed it. God will exalting believers that humble themselves (Ps. 37:34, 92:10; Mt. 23:12). Paul drew on Old Testament terminology (Num. 33:55; Joshua 23:13)

Paul did not have a pride problem but God assured it would not develop, so he allowed a continual buffeting. A devil was Paul’s "thorn in the flesh, " a messenger of Satan to continually buffet him so pride would not take place and he would be exalted. Whatever he saw and heard he kept silent on it for 14 years until he explained this.

Thorn- Gr. skolops occurs nowhere else in the New Testament. It means properly anything pointed or sharp, a stake or palisade… The word is used in the Septuagint to denote a thorn or prickle.

What was it? Certainly it was some physical malady that persisted. All sorts of theories are held (malaria, eye-trouble, epilepsy, insomnia, migraine or sick-headache, etc.). (from Robertson's Word Pictures in the New Testament)

The most logical is that it was probably a bodily malady, because of his statement "in the flesh;" It was some bodily affliction that continually bothered his flesh, not his ministry.

The Greek word for "messenger" here is "agellos," and it is an 'angel'. A fallen spirit (of Satan) who can only be allowed by God for the believer. In Paul’s case this was unique and different than the other apostles and this is why it is not just about being persecuted (which is promised to all believers 2 Tim. 3:12)

This is further explained by “To buffet” which means to strike with the fist, it is related to physical violence (what was done to slaves). The thorn in classical Greek was in the sense of a pale or stake (Vincent’s Word Studies). Paul was plagued on and off with this continued bodily affliction. The source in this case was Satan's messenger, which many suggest may have been a personal physical affliction not only the constant opposition of those hostile to him.

The Hebrews would attribute severe and painful diseases to Satan; such as with Job 2:6-7. Paul says it was given to him, in other words God was overseeing it like Jobs. Satan is often attributed to be the afflicter of the body in the New Testament. In the gospels demonic activity is often accompanied with pain and some form of disease (Luke 13:16; Acts 10:38). In Vv.9-10 Paul laments “Concerning this thing I pleaded with the Lord three times that it might depart from me. And He said to me, “My grace is sufficient for you, for My strength is made perfect in weakness.”

After he requested three times for the Lord to remove this physical malady Paul was not healed. It was in his FLESH, it was a PHYSICAL infirmity and Jesus said NO to his request for healing all three times. The Lord answered NO to Paul. Not all God’s statement are yes or amen.

Instead, God’s had determined Paul’s afflictions (He was given to me.) God appointed it and God’s grace was there for his malady, for only God would want Paul to keep humble, the Devil would want him operating by pride. Paul had to surrender to the will of God in his situation. God said NO to Paul’s request for healing because God had a greater purpose in saying no. Paul understood the benefits; it brought dependence. He had a messenger from Satan to live with. It was God’s will and he accepted it. God’s answer was His grace. God’s power was then exhibited in Paul’s life because of his affliction.

Paul reiterates his infirmities understanding we are given a weakness so that we can be more dependent on the Lord and He will be glorified in our weakness. “Therefore most gladly I will rather boast in my infirmities” …“Therefore I take pleasure in infirmities, in reproaches, in needs, in persecutions, in distresses, for Christ’s sake.” This was so “that the power of Christ may rest upon me”… “For when I am weak, then I am strong” (2 Corinthians 12:9-10).

Paul’s obstacles in his life became his pulpit. He was able to preach Christ with more conviction. His weakness was a physical handicap, and the result of this suffering kept him continually broken and dependent on the Lord’s grace for strength. Infirmities, Astheneia in Greek; means a feebleness that has to do with strength, a weakness in the mind or body. This can be caused from disease, sickness, (used in various places like Matthew 8:17; Luke 5:15, 13:11; John 5:5; 1 Timothy 5:23). Paul’s weakness became his asset. This human flaw he possibly carried throughout his whole ministry after seeing heaven became an opportunity for God’s strength to be manifested, and God was glorified. To the Galatians he said “You know that because of physical infirmity I preached the gospel to you at the first. And my trial which was in my flesh,” Paul goes on to say “For I bear you witness, that if possible you would have plucked out your own eyes and given them to me” (Galatians 4:13-15, 6:11), alluding to the kind of affliction Paul had with his eyes and the compassion they felt for him. So God can use even those who are weak and sick, sometimes more than those who are physically healthy and strong. 

We find that the Lord will break someone and allow suffering so that they can have compassion for others and be used for His kingdom. We are purposely brought through the valleys, so when we get to the mountaintop we can be useful to others who must tread through the same valley. This is one of the reasons God became a man, to identify with us, as Jesus was perfected and brought to His goal by His sufferings. We now have a “High Priest made like his brethren, who can sympathize with our weaknesses. For He Himself has suffered, and was tempted as we are, yet without sin to aid those who are tempted” (Hebrews 2:17-18; 4:15). God “comforts us in all our tribulation, that we may be able to comfort those who are in any trouble, with the comfort with which we ourselves are comforted by God. For as the sufferings of Christ abound in us, so our consolation also abounds through Christ” (2 Corinthians 1:4-5). Suffering has value in that those who have gone through it can minister comfort to others who also suffer. Our sufferings and hurts build compassion in us for others, and we are able to minister healing to them. All true leaders will have this same similar journey to be ministers to others.