Pedalling efficiently requires a stiff interface between your shoes and the pedals. The best commuter cycling shoes will have a stiff midsole to help you ride more comfortably and transfer power to your bike more effectively.
Although the best flat pedals for cycling will work well and mean that it's easy to get a foot down at stops, you'll get greater pedalling efficiency from a set of clipless pedals, where your shoes connect via a cleat with the pedals.  We've got a guide to riding with clipless pedals if you want to know more.
For commuting, two bolt SPD pedals work better than the more race-oriented three bolt systems. Two bolt pedals normally have two sides on which you can clip in rather than one, so it's easier to get moving and the smaller cleat is recessed into the sole, so they're much easier to walk in.