From what I've been told (guy I work with who used to run Northwest's Full Motion sims, with about 900 hours in them), it depends.
Once its off the ground, and you just want to fly it, that's not that hard. I've been told its just an issue of practice, and the theory holds true for anything.
The problem with using something like MS Flight sim is it doesn't model a real cockpit, and "takes care" of a few things for you. Its by far not the most realistic sim out there.
For what they did, I would imagine that with some time in a full-cockpit simulator, most pilots could emulate. The harder part comes from the Navigation. Some navigation was done to get there, and while on that morning the towers would have been visible from a long way, they seem to have made mostly a beeline.
They turned off the transponder, but apparently didn't pull the circuit breakers on the CVR.
Its going to be harder than MS Flight Sim shows - after all, that's a game. (Its very handy for things like Instrument Practice, its been remarked that with flight sims, and those of us used to computers, piloting's getting lots better with instruments - during my flight test, the Examiner asked if I'd done a lot of flight sims, because my instrument flight was well inside IFR tolerances, which are tighter than the VFR I had to pass)
So.. harder than he thinks, but not that hard if you've practiced in a real sim for the suicide run. I tend to think that the bank on the second plane was due to a mistake rather than a deliberate attempt, but... we don't know.
Addison