While I have only done one duathlon as a team a few years back, it would seem to me the way to go is to change shoes. If you were to wear runing shoes, you may save time in the transition area, but can you really pedal as fast with running shoes as with cycling shoes? I don't think so. You'll make up whatever transition time you lost while changing shoes before the ride, by riding with clipless pedals and cycling shoes. Your power transfer to the pedals will be much more efficient. Good luck, Gino