I'm assuming we're talking about a military version of the Boeing planes or something that looks very much like them. I think it makes a remote control theory much easier, particularily if a smaller drone was used for the Pentagon strike. That said, however:
If military planes/drones were used, why did they shoot down Flight 93?
If the planes were just holograms, why didn't they use the correct Boeing planes instead of these military models, as seen or photographed?