If you plan to go on long rides, you will really want pedals with a wider platform to help avoid getting hot spots on your feet as well as shoes with stiff soles. Shoes designed for walking will usually not be as good when riding.

Speedplay and Shimano SPD-SL systems work well.

If you go with SPD pedals, the new XT and XTR pedals have more pedal/shoe contact area, but they will cost more than other options. I was out on a few hour MTB ride last weekend using new XT pedals and Pearl Izumi shoes with a carbon sole, and the combination felt pretty good. The shoes were also walkable.