So what about your arches? It is very common for the arch to compress or collapse with each pedal stroke as the foot presses down and compresses in the shoe. The degree of collapse will be affected by the amount of power being transmitted and varies from person to person. Limiting the arch compression can do wonders for knee, hip and lower back comfort. Most cycling shoes come with inadequate foot beds and little to no arch support (one of the brands we sell actually has a very nice footbed system). Most cyclists will benefit from a "mildly intrusive" amount of arch support. When standing in your cycling shoes it should feel like too much but once you ride for a bit you should cease to notice it. There are a few aftermarket footbeds I have experimented with which we do not stock at the store but my favorite so far is from eSoles. They have a modular arch support system (which Bontrager uses a cheapened version of) so you can try varying degrees of support. If you already have high-ish arches you should make sure to get the black arch support in addition to the kit as it is the highest but doesn't come with the kit. Superfeet and Sole make good products as well.
Now the disclaimer: If in doubt, get the advice of a professional. If you change something and it hurts, put it back. Now go out for a bike ride!