Does the playcalling system take anything into account other than the orders called. I.E. will an intelligent QB notice that it is 3rd and long and try to pass?

I don't think so!
I noticed this specifically today when orders to "prefer the run" had a first drive of..
Pass - Incomplete
Pass - Incomplete
(3rd and 10) Run - next to nothing
Punt!

I don't want to turn into the Minnesota Vikings but Run, Run, Pass would have been a prefered opening drive, even if they mixed it up later on in the game