I agree that AQ has become a convenient catch all label for any Sunni Jihaddis, but the fact that much of the so call AQ "leadership" KSM, Omar Saeed Sheikh, etc. were ISI assets is very significant and too often is curiously dismissed or ignored. When it comes to terrorism in Kashmir for example, the jihaddis or "Al Qaeda" were not operating, financing and recruiting on their own, they had state sponsorship.
Have you read this?
http://www.amazon.com/Deception-Pakistan-United-Nuclear-Weapons/dp/0802715540