If you look at just the 21st century with our current system in place...
On the men's side, the US has won a silver (Meb) and a bronze (Rupp). On the women's side, they've won two bronzes (Seidel and Kastor). So the U.S. has won 4 of 36 available marathon medals in the 21st century: 11%.
Also in the twenty-first century, the U.S. has exactly one of the top-200 fastest men's marathoners-- Khalid Khannouchi at 2:05:38. That #153 on the list of fastest marathoners since 2000s (legal courses/times etc.).
On the women's side, the U.S. has Sisson at #36 in the 21st century, followed by D'Amato at #50 and Kastor at #62. They have nine of the top-200 fastest women's marathoners in the 21st century-- so 4.5%, which is half the rate at which they've been medaling.
If anything, you have to acknowledge that the U.S. teams have overperformed in the Olympic marathon relative to talent level. I really don't understand the problem needs to be solved here.