Aside from the obvious (the worst thing that can happen in the sim is that you fall off your chair), the biggest thing for me is the mental side of it. I don’t spend any time while simming listening to the engine. In the real airplane I am constantly listening to that thing. Does it sound right? Was that a little cough? And then when you get, “Cherokee 125, traffic 11 o’clock and 3 miles, type and altitude unknown”. Pucker! It’s just hard to describe. It’s one of the reasons I don’t believe in using sims (approved sims/FTDs) for instrument currency.
The physical/mental side of actual flight cannot in any way be recreated through simulation. Don’t get me wrong, sims are great procedure trainers. But as far as the comparison to actual flight, that’s all they are. Procedures trainers.