I'm new to CFS3 and have been playing around with the Mission Builder to create B-17 missions that I can fly. I can't help but notice that, quite apart from the aircraft that I place into a mission, there seems to be lots of other allied and enemy aircraft flying around that are independently generated by the game engine. 
For instance, I tested one night mission over the channel, where the Sim sent up some German Night Fighters against me; and when I took a flight of B-17s to bomb Bremen, I bumped into another flight of B-17s in the same area. What was really cool was that I was flying the Avhistory Molly II, whilst the other flight was the Memphis Belle, which I had installed from Just Flight.
It seems that CFS3 is probably a lot more sophisticated than one might imagine, and certainly makes Mission Building a much simpler process: All you have to do is select a mission target and create a flight of aircraft to go there, and not only will CFS3 send up some bad guys to play with you, it'll send up some good guys too.
This is a major leap forward from CFS1 and CFS2, and I'm seriously impressed.

Thanks for confirming my findings. Now I know that I'm not completely insane. 8)
I don't wish to recreate historical events - just recreate a flavour of the times. I like the surprises.
However, thanks for telling me about your programme, it may come in handy some time.