I have performed work in the pentagon, and I am surprised the plane caused as much damage as it did. It would take something that large, and with as much momentum, to cause such devastation to that building. Any pieces of the plane that were left over were most likely taken directly into forensic labs, and that's why we didn't see them. Come on, there are much better buildings to blow up than the pentagon; the terrorists just didn't do their research. Even a domestic terrorist, if you believe that's what this was, would be smarter than that.
Also, a cruise missile explodes outside of it's target to induce the most amount of outward damage, similar to a torpedo. Whatever hit the pentagon burned more than exploded. If it were a missile, there would be much more chaos outside of the building. Our weapons work very well, and would have caused more extensive damage. Not to mention the idea of anything else seems idiotic.