Not much that I can add that hasn't already been said. I have a Hybred/Mountain bike and a couple of road bikes, All of them are 2 bolt SPD. When I first started getting more serious about road bikes but was not in very good physical condition, I appreciated the "walkability" of SPD cleats. I live in the hills and walking a quarter mile up a hill along the road in 3 bolt road shoes is not fun. So my early road experience confirmed my decision to stay with SPDs was a good idea.
Now I'm in much better shape and will not be walking uphills so much. I have thought about switching over to a 3 bolt systems. I mean I have thought about this a lot. So my contribution to this discussion is that which ever way you decide to go you will probably spend a considerable amount of time second guessing your decision. But as far as function is concerned they are similar. I think outside of the difficulties walking with 3 bolt, the biggest thing is which style of cleat and to a certain degree which shoe do you prefer? Mainly in my opinion it is a fashion decision. A lot of roadies use SPDs I will say.