I good insole can make all the difference. The most comfortable I've found for myself are ProFoot Miracle Insoles.
I have narrow, bony feet with high arches and lifelong problems with foot cramps from inappropriate arch support -- too little and too much are just as bad.
My Scott Road Pro shoes came with good looking, kinda techy insoles with detachable arch and metatarsal supports, but I just couldn't get comfortable with that insole. Besides arch cramps I had hot spots during hard efforts in group rides -- very disconcerting, having to suddenly stop pedaling and coast, or to find a safe place to pull off and stop during a group ride.
I tried several Dr. Scholl insoles I already had that were comfortable in walking shoes, but none of them was quite right with the bike shoes. But the ProFoot insoles have been excellent for more than a year -- well beyond the recommended wear period of 3 months, although that probably presumes regular walking rather than cycling 200-400 miles a month.
I just got a pair of Fizik Tempo shoes with insoles that I can already tell won't work for me -- too rigid, not enough arch support. So I'll probably buy two sets of ProFoot insoles this week.