I thought that it was remarkable that a passport belonging to the alleged leader of the hijackers (and lots of bits of aeroplane, passengers and crew) managed to survive at the WTC site - but the one hitting the Pentagon not only vapourises but shrinks considerably on impact!
Take a look at any air crash imagery and you will invariably see the fin in fairly recongiseable - even if it has just flown into the side of a mountain.
I'm not an expert by any stretch of the imagination but I would have thought that the material of the buildings that the aircraft flew into would have a huge impact (scuse the pun!) on the resulting remains.
My understanding of the twin towers was that they were designed so that all the strength of the building came from the central core which housed all the services/lifts etc. All the office space was then effectively bolted onto the centre and a light curtain wall of glass and concrete/steel made up the exterior.
The pentagon was an entirely different construction, Solid brick walls which I would imagine are considerably thicker than the WTC. Not to mention the fact that as the centre of the US military machine the pentagon would have been targeted by a not inconsiderable number of nukes and I'm pretty certain they would have designed a bit of strength into the building.
Bearing this in mind it's not difficukt to see how you could get a large amount of wreckage/debris from one attack and not very much at all from another.
To highlight this I do remember seeing a programme about crash testing stuff. One of the tests was on the proposed design of the wall to protect a nuclear power station (similar to the design of the pentagon I would imagine)
To test the wall they built it at the end of a two mile test track, at the other end of the test track they got an ex mil F4 phantom, they then fired up the engines and launched teh F4 along the track. by the time it got to the wall it was doing quite a bit more than 200 miles an hour, the hi speed film of the impact was spectacular, all you saw was the F4 vanish in a cloud of flame and dust, the airframe was practically vapourised and all that was lef of the aircraft were a few shards of metal and the very tips of the wings that had been sliced off by the edges of the wall, the wall itself had a bit of a small bump and a few scorch marks.