I highly recommend insoles (like Superfeet) and a metatarsal button. (not a met cushion, but a met button. if your shoe store doesn't know the difference, run away!)

Sometimes the metatarsal arch squishes down under the pressure of cycling (cuz all your push is running through your forefoot). If you are someone with a dropped met head or neuroma it can be REALLY painful. When that arch is squished or already dropped the nerves that run through there get compressed and misery ensues.

I was having terrible left foot pain with my Specialized Tahoes and my Speedplay Frogs. Put green Superfeet and met buttons in both shoes, and no problems since.

Superfeet berry and orange have low met buttons built into them, but they aren't beefy enough buttons for some folks.