I think your take on the ISI is well placed. I think the Pak govt serves at the pleasure of the army, while the ISI upholds the agenda of the "true believers", while allowing the govt and army "plausable deniability".

Every so often the ISI will provide a scape goat and talk about reform.

The bottom line, IMO, is Pakastan's pathological fear of India. That fear determines Pak foreign policy. If Pak continues to see US policy as favoring India we can only expect more "disappointments" from Pak.

The bad thing is that it seems to me we have yet to determine what we can and will accept as an achievable end state.
Unfortunately, others are not operating without a strategic goal. Events may pass us by while we try and figure out what to do. The SCO grows, while NATO shows it's impotence.
http://www.atimes.com/atimes/South_Asia/JL09Df02.html

Since about 1965 China has been Pak's most important strategic partner, while USSR/Russia has ebbed and flowed with India. I don't think the GWOT has altered the China/Pak relationship at all.

I read these recently and thought there were some interesting points.

http://www.atimes.com/atimes/South_Asia/JL06Df03.html

http://www.atimes.com/atimes/South_Asia/JL09Df01.html

Some people don't like the source, but I think it provides a good start point to do further research. I think the region gives a new meaning to "Byzantine politics". Just 2cents from someone trying to learn about the region.