Other really fun things to consider:
-shockwaves - anything moving at trans-sonic speeds will already encounter Mach+1 airflow velocities at some points on their wings and fuselage, even if the indicated airspeed is less than Mach 1. Propeller blades are a good example of this; it's also the reason why helicopters are fundamentally limited to velocities lesser than Mach 0.5. Thankfully, FreeSpace doesn't have propellers... so propeller torque will not need be taken into account.
-vortices (induced drag/wing tip vortices/wake turbulence), and I'm not talking about the difficulty of modeling turbulent airflows. As an example, a very large portion of lift generated by the Concorde's wings is due to large stable vortices on top of the wings reducing the air pressure there. So lift is not exactly always just a function of angle of attack and airspeed in laminar airflow...
-shifting of aerodynamic balance (center of pressure) in different velocities. For example Concorde dealt with this by shifting it's center of gravity accordingly by fuel transfers.
-stress factors depending on flight state; overspeed and pulling over-g's comes to mind first. You'll likely also want to implement blackouts and redouts somehow. For example, even if the ship itself can handle re-entry, it's unlikely that the pilot can handle the rapid deceleration if the ship were to, say, turn sideways or enter uncontrolled spin.