Here my opinion differs from ag's however: he equates the State Dept. with the entire Bush Administration. I contend that there is a great schism between the "hawks" (Cheney and Co.) and the "realists" (Gates, Rice, et al). Not that any of them have particularly exemplary records, or intelligence, or proposals. But they are radically different, IMHO. Cheney's team was dead set against a recociliation between Bhutto and Musharraf, and would favor reimposing military rule - martial law - and indefinite postponement of elections in favor of keeping Musharraf in power.
I wonder how much of that "schism" is for show, and how much is real. I doubt that their differences have led to any serious changes in how US policy is brought about. I frankly cannot think of a time where we can clearly point to A) and say, this was VP Cheney, or B) this was Sec.State Condi's input.
part of the problem is that the whole WH controls the message far more than controlling their decision-making, and regardless of who won (if anyone) their message machine is there in spades.