Pride seems to be what many think was the "thorn".
The term " thorn in the flesh" or thorn in my side as used in the old testament most often stood for persecution from your enemies. Paul is asking the Lord to remove the Judaizers from coming behind him, and trying to put his converts back under the law. It was'nt sickness, and it wasn't homosexuality for God's sake!
There are many evidences within his own writings that his thorn in his flesh was his eyesight.
He was roundly abused and stoned a number of times, even left for dead once.
His ending of the letter to the Galatians, I believe, is "see what large letters I use." Assuming that the large letters were necessary because he couldn't see small ones, and assuming that the stonings might have also hit his face and injured his eyes, then the "flesh" that needed repair would have been eyes.