The lacing area and tongue should be padded, especially if you have bony bumps on your instep. Be sure the sole flexes easily where your foot flexes. Buy shoes with removable insoles so you can modify or replace them with orthotics. Allow a half-inch in front of your longest toe when you stand up. Fit shoes in the afternoon or after a workout, when your feet are larger.
Feet swell as much as a full size during a good workout.
The key to finding the best shoes is comfort, not price or brand-name. Don't rely on a break-in period. Shoes should feel good the day you buy them. The toe box should allow your toes room to move around. The mid-part of the shoe when laced should hold your foot snugly so that it doesn't slide forward and jam your toes with each step.