I did a Duathlon yesterday - 5k run, 25k bike, 5k run. My bike has flat pedals with strapless toe clips, so I just wore my running shoes for the whole event. Almost everyone else was using clipless pedals.
If I switch over to clipless pedals, I'd need to change shoes twice during the event. I think that would cost me about a minute in total. Would I make up that lost time on the bike by using clipless pedals? I was just over 50 minutes for the bike leg, so I'd need to be 2% quicker for it to be worth it.