That looks like a great commuter set up. When I started commuting again on Long Island I used my bike with 700c wheels. The potholes, irregularities and garbage in the road caused me to rethink and use my 90's Trek 800 mountain bike. The mountain bike was heavier, but took everything in stride. I put smooth tires on it but kept the flat bars.

One of the big advantages of 559 wheels is that they are strong. Really strong. The only thing stronger is BMX wheels.

I wouldn't change a thing. Ok, maybe skinner tires, but I believe you got those for the ride and I would be inclined to think that that may be a good way to go especially if you are seeking more comfort.

In fact, one of my thoughts while I was commuting is that a suspension fork with only a little bit of travel would be a good way to take some of the jolts out of the ride. But fat tires might be a better way to go.

The fact that it is non-descript frame is a plus as far as I'm concerned.