One thing that never fails to amaze me about running shoes is how such a precision designed tool, with so much research and development thrown into it, can always come with the flimsiest and least effective insoles imaginable. This is not an indictment on any one company; I can not think of any that do not ship their shoes with really bad insoles. Now, for 80% of the people that buy those shoes, the insoles may be perfectly fine. In fact, right now I still always use the same insoles that ship with my shoes. Something that you may want to consider, especially if you have arch problems, is replacing them with something like Superfeet. Insoles like that provide a hard plastic shell under your arch which helps support it and can really reduce pain from injuries such as plantar fascitis. If your arches hurt, visit your doctor to see if he or she thinks that they might be right for you.
Whatever you do, though, do not put something like Spencos or Dr. Scholl’s in your shoes. You do not want to provide less support for your arches while you are running; that is just inviting your foot to hurt itself. The gel might sound like a good idea, and maybe when you are sitting at your desk at work they are, but it does not let your foot get a feel for the ground and you stretch your arch out in unnatural ways while you are running. If you have any questions about arch support and insoles, you should consult somebody with experience such as your local running expert and your doctor.