I've owned several scooters, a KLR, and quite a few other bikes. There are seven in the stable just now. Running a KLR on pavement for daily commuting in the city/suburbs makes little sense. If you have rough pavement, gravel, and moderately rough trails, the KLR shines. It is not a trails bike. It is not a road bike. It's a rough-road all-rounder.
A good scoot is a joy carving up suburban pavement. The work load is low, and they just eat up traffic. They are truly fun to ride, and the storage and slop protection speak for themselves.
However, on anything but good pavement, the roles reverse. Here, I was getting beaten up by my scooter (Aprilia Scarabeo 500ie). Our roads are crap. I actually find the KLR a very comfortable commuting machine for this area. In other parts of the country, with different road conditions, it wouldn't be true. If you don't need off-road capability, why have it?