Agree that Specialized insoles are good although I only have the non-custom €30 ones with the metatarsal button. Maybe their shoes are good too, but I haven’t been able to afford the ones I like the look of. The Body Geometry insoles postpone discomfort for me, presumably because they spread the bones in the foot, which leads me to:
Having been through a lot of shoes and pedals with similar problems, my impression is that width across the forefoot matters more than anything else. There needs to be a wide, flat floor there for your foot to splay unrestricted as it does when walking barefoot.
The best shoes I have found for this are those by Northwave. Shimanos are poor: even the wide-fit models are narrow across the ball and curve upward at the toe (inside) like a ski, which is an unnatural position for my foot to repeatedly exert force in. Shimano shoes have acres of room at the heel where it makes no difference one way or the other because the foot doesn’t move there.
For the most part, cycling shoes are terrible things: inflexible when feet should move, with artificial materials that don’t break in; too narrow at the front (for what earthly purpose, given that cycling exerts negligible sideways force on the foot unlike other sports?); too much faux ergonomic shaping that healthy feet don’t need; ventilation that no-one asked for; and too high around the ankle and up the back of the heel in search of unnecessary and unwanted support that irritates ankles and Achilles tendons.
Vivian Grisogono’s brilliant self-help book on sports injuries lists basically all the features of contemporary cycling shoes as causes of injury. No wonder so many cyclists have foot problems.