Here's a nice tip about swapping factory insoles for a higher quality set. It's amazing you cand drop $100 for some good trail shoes and end up with flimsy cardboard for the insole! For a couple years now I've been using insoles like this by Abzorb (I get mine at New Balance) for my trail shoes and placing the standard shoe insole into my bike shoe -- a bit of cushioning in the bike shoe can make a bike difference, particularly for any hike-a-bike situations.
Remember the insoles don't last forever and wear down with time and mileage