I'm a fan of either a stiff soled shoe with clips, or clipless SPD shoes, depending on my mood. 99% of the time I ride though is with my SPDs. I have a pair of Giro Republics that I LOVE for faster rides and also typically wear these to commute to work. They're decent walking shoes, but you can tell they're made for biking. There's almost zero flex in the sole, which is killer on rides, but what makes them walkable is the way the bottoms are constructed. The elevations on the bottom of the shoe create a rolling-like movement that facilitates walking. Not good for a hike, but fine for coffee shop outings and for getting me to my desk, where I have pair of sneakers under my desk (I do a lot of walking/standing at work, so staying in the Republics isn't a good option).

Alternatively, I used to ride in a pair of DZRs (Jetlag | DZR) to commute to school. This was back when I didn't have a dedicated space to store stuff though. I never use these anymore, but have logged over 2K miles on them. I'm thinking about getting a pair of these when school starts up again so that I don't have to stop by the lab to change shoes every day: Jetlag Nero | DZR The fact that they're a slip on also adds to my personal "gimme gimme!" factor. I like the idea of just sliding 'em on and heading out the door.

Now, to speak to foot pain: On longer rides, the DZRs would create hotspots. They're meant to function well as a walking shoe, so there's a decent amount of flex in the sole, that I think disrupts the even spreading of pressure on your feet -- the way a plastic plate like those found on the Republics does -- creating "hotspots." I've taken the republics out on 27 milers with no such hotspots. Regarding your metatarsal pain, I would imagine keeping your foot movement restricted would provide a more comfortable ride. I think a good mountain/road shoe with a good fit would probably help. I would look for something with a stiff sole though. I would Chuck Taylors are going to flop about way too much to provide much comfort in your situation.