I was getting acute pain in the ball of my left foot on any ride lasting more than about 40 minutes. I put this down to a combination of leading with my left foot when setting off and that being the location of the SPD cleat plate on the shoe. My right foot would also hurt in the same location after about 90 minutes.
Since I am unable to alter which foot I prefer to lead with, and even if I could I would merely alter which foot gets painful first, I decided to try changing the pedal system I use to one with a larger cleat in an effort to spread the load of medalling over more of my foot and thus eliminate the point-loading which I assume is responsible for the pain. Unfortunately none of my existing shoes are drilled for fixings other than SPD, so I am unable to isolate the effect of changing cleat size from the effect of changing shoes. Since I have the same problem in both my pairs of SPD shoes, one of which is a Specialized Body Geometry Pro MTB (2006 version of these), I don’t think that the shoes were the problem.
The pedals I chose to try are Speedplay Zero in blue to match my OpenCycleTeam jersey; I picked the Chrome Moly material as they are cheapest and only differ from the others in mass (wiggle sell them here). Shoes are dhb R1.0 in red/white. Final piece of the puzzle is cleat covers: unlike SPDs the cleats stick out and will wear if you walk on them, so these save you buying replacements too often.
The changes seem to have worked, in that the pain is gone. I like the Speedplay Zero system because I can adjust the float so that I never hit the limits while pedalling, I can adjust the centre position to how my feet naturally want to move as I pedal and unlike every other pedal system I’ve seen there is no spring-force from the pedals trying to make my feet move to the centre (AKA move in the way the pedal designer found most convenient to handle).
The shoes are fairly comfortable; my only gripe is that the cleat holes are drilled at a very heel-in angle, to the point where if you pedal in the plane they are set up for your heel will tap the chainstay. I have to set my Speedplays up to allow a lot of heel-out to compensate; if I were using a less-adjustable pedal system it would be a real problem.