Sole and/or upper flexibility might be an issue, either normal, or age-weakened. I have a different, but possibly related issue. I have a hammer toe that is a bit higher than the others, and for certain shoes when they flex the top material flexes right at that point and can irritate the top of that toe. It actually got fixed when I added carbon fiber shoe plates - not for that issue, but it was a bonus.
Should be pretty easy to check if your shoes are touching your toe nails during your stride, and where. Deeper as well as stiffer may help.
Edit: Humm, I'm wondering if metatarsal pads might help for this as well. buy some and stick the m on your insole - make sure you put them in the right place behind the ends of the lone bones in you feet. The net result should be the you toes may bend down marginally more during your stride. All things being equal, however, bigger shoes of course.