For follow-up discussion and general commentary on the topic. Comments are sorted chronologically.
We will never be able to understand some things while on this terrestrial shore, but thank God that knowledge will one day be completely swallowed up in omniscience and then we shall all understand without questioning what Paul's thorn in the flesh was.
Is it possible that Paul is talking of an attitude, a behaviour or action he regrets indulging in and which he knows is not Christ-like? He may have been struggling with such without success and had asked God to help him only to get that answer. Anger, for instance.
I believe that Paul's thorn from the Messenger of Satan was that when Stephen was being stoned, Paul was holding Stephen's cloak. I believe this came back to haunt Paul because of the life he had lived before his conversion.
I believe Paul was talking about a physical ailment. I don't think he was speaking of a spiritual problem that haunted him, such as anger, selfish ambition, or envy. If that was the case he would have said THORNSSESSES.
He's talking about a backache, or an ankle that gets sore every time he jogs, or a wrist that keeps him from doing push-ups. I don't know of a worse thorn in the flesh than arthritis. I guess it comes to mind if you suffer from it.
Arthritis is painful, and it affects multiple areas of your body (flesh). The description of the problem as a "thorn" makes me think it had something to do with pain being associated with it. A problem with your eyes would probably not be called "a thorn in the flesh." Neither would an emotional issue, in my opinion.
Arthritis gets my vote. Maybe it's because it's my thorn.