Boogie-nicey,
I somewhat second that. As a child aviation enthusiast the first and main access to a stick and rudder I could get was through the various, basic, flight simulators on offer on PCs. I wouldn't for a minute say their fidelity is accurate but the basics of reacting to changes in pitch, yaw and roll with pedals and hand movements are universal (why else would we consider light aircraft training a useful precursor to bigger and better aircraft?). Likewise correlating that to various changes in basic aircraft instruments and reacting accordingly became second nature.
I never throught it would necessarily improve my flying, but when I first undertook flying training, initially on gliders then powered aircraft, my results were tremendous. This cannot be some inate ability so the only thing I can put it down to is the practice I gained at keeping needles lined up while playing my old computer simulators. Microsoft FS was one of them.
I think there is a degree of elitism in denying the value of these as training aids. Some of the products available make accessible to the general public information that would have been completely unavailable previously. That in itself takes away some of the mystique of something a few would like to consider their exclusive and elite domain.
The basic Flight Simulator program itself is very limited. The addons on the other hand incredibly detailed in systems, presentation and possibly handling. I suspect critics of the system are maybe unaware of what these external addons offer - a few of them have been listed above.
As an aside, I have been using a soaring simulator for off-season gliding which has been fantastic for keeping the stick and rudder skills from rusting over. The latest copy of Sailplane & Gliding featured an article on Lasham GC using a simulator for training an ab-initio pilot as a trial. The results appeared to be brilliant, with the instructor commenting that by his second "live" flight the student had unprompted control throughout and flew something like a slightly out of practice, solo-standard pilot.