There's a simple answer.
No matter how good the physics modelling etc - which at this stage of flight sims, on the top of the range programs, is excellent - there is absolutely no aspect of any simulation that engenders the same emotions in yourself, and tere is no simulation whatsoever of the physical stresses.... there's a world of difference between greying the screen out at 6g and actually being anywhere near 2g in reality. (2g is probably in excess of anything I ever experienced, apart from an aeros trip I had shortly after the Be2D was phased out of service).
In the sim if you push forward and go negative g you might get some onscreen effect - in real life your tummy goes funny. There is a world of difference between pushing buttons, flipping switches, and making decisions in front of a screen and doing it with a barf bag in front of you.
Just ask a kipper fleet wet man from 20 years back what stage 2 was like when your tummy didn't feel all that great, or anyone who ever flew a MAD comp <g>
They are all PARTIAL simulations, very good at what they do, but they don't simulate the full experience so will never take the place of genuine flight. That's why we have ground simulators AND training sorties in aircraft/exercises.
Dave