Speculation-

Engines - more thrust?

Airframe - hardened and strengthened to withstand greater G forces for better maneuverability?

Communications gear to survive any type of EMP/nuclear event?

Advanced radar and potentially radar jamming gear to confuse missiles and enemy aircraft?

Weapons systems - air-to-air and/or air-to-ground missiles?

Obviously a nice custom interior with its own security features to protect the president.

I’m just guessing - but something, or multiple things, have to account for an extraordinary price.