I am not a resident, so the more experienced members of the group would probably be most able to answer your question, but I'll give it a shot.
Combined AP/CP is 4 years in length, and I think it's the more popular route to take; having the combined certification can make you more marketable.
AP or CP only are each 3 years in length. I think I remember reading on this forum that AP only may be useful for someone who strictly wanted to practice academic pathology...maybe someone with a little more knowledge could add more info (or correct any wrong statements)?