are you sure the instep discomfort isn't from having the straps too tight?
typically over the course of a long ride i will need to loosen my shoes up a little as my feet swell.
i like stiff carbon mtb shoes for the efficient power transfer but being mtb shoes they still have a little bit of tread on the soles that alllows moderate comfort while walking. softer soles give me "hot foot" after a while from the cleat digging into my foot.