Hi there, new member to the forums and an orthopaedic surgeon so just though I'd throw my opinion in there.

Just to get the terminology straight, the long pin or rod along the bone is a nail, the small pins at each end are screws that go through the nail (called locking screws).

The concern your surgeon has is that in the event of another accident you could break at either end of the nail, meaning a very low or high fracture which is difficult to fix. Worst case scenario is that you could break mid shaft of the femur and the nail would bend, making it difficult to remove (which is required to fix the new break).

I tend to avoid removing metal work, any aching or soreness is not garunteed to improve, you weaken the bone slightly when you remove the screws (empty screw holes in bone take about 6 weeks to get to the same strength as screw holes with screws in them), and there is the risk of anaesthetic etc., remember that in the States removal of metal work is financially renumerated so it is performed a lot more commonly than in Europe. That being said if you are in high risk activities fixing a break is a lot easier if the nail isn't there. If you do a lot of cycling on busy roads, or any of roading then you would probably be safer removing the nail.

I should mention that I have not personally nailed a femur or tibia in a cyclist during the past 5 years, and i'm on call every 5th day.