The biggest issue with the "War on Terror" is that it involves a lot of hazy handwaving, amibguous goals, and very little practical evaluation of what gets results--i.e., it shows all the signs of being a political power grab masquerading as the solution to a (potentially real) problem.

You're probably already familiar with him, but Bruce Schneier has written at some length about ill-considered counterterrorism efforts on his blog.