I've now gone from a size 8.5 to a size 7 after two years of running 55 miles per week, when I previously ran less than 20 miles per week as a teenager and in my twenties! That's got to be an abnormal level of shrinkage right? I was pretty flat-footed to begin with, but its hard to imagine my arches would raise that much.
So did you go down a shoe size when you increased the miles? Have you just been wearing the same shoe size out of habit? I say this because I just went to the shoe store today for the first time in a while and was forced to try a size lower than typical due to availability, and crud, they fit better. It wasn't just the brand. I then proceeded to try on that size in every brand and they were much more comfortable. I know this size was not more comfortable 10 years ago. I am 35.