lineshot,
I think you're probably right when you point out the bigger workload Prior faced in his first year in the bigs. As we know, except in the case of Clemens, Nolan Ryan and a few others, there is a cumulative effect on the body after throwing so many pitches. Either it's the elbow or the shoulder that suffers. However, unlike Kerry Wood, Mark Prior is very physically fit in terms of his legs and his core. That is another reason why his arm problem is puzzling.
As Dr. Andrews told my son last June, Jordan, just be glad that you're here for elbow surgery and not shoulder. Recovery from shoulder surgery ie. torn laburm, torn rotator cuff is much more iffy than Tommy John and the elbow. I can only pray that he is correct in our case.