I don't have experience with metatarsalgia, but I have had experience with metatarsal stress fractures, ruptured plantar, PF, etc. Basically any injury I get is in my feet.
I haven't had any problems in 14 months or so, I routinely do foot strengthening exercises. All of these are done barefoot.
Toe walks (normal, toes pointed in and out)
Calf raises
Standing on one foot for 1:00-1:30
Rolling a golf ball underneath both feet
Toe scrunches
Barefoot strides (on grass obviously)
Stretching religiously (calves, hammys, quads)
Hope this helps.