One thing that always stands out to me is the way trim works in the sim is nothing like real life (for aircraft with mechanical linkage that is, not fly by wire. I think. Never had the privilege to fly such a thing IRL). In the sim your joystick always returns to the same point, in a real aircraft the trim changes where the yoke stays put. So if you want to climb you pull up then trim until the yoke stays pulled up. In the sim you have to return the joystick to neutral as you trim. I’ve always hoped this would be solved with some kind of force feedback yoke (well, I’ve seen one out there, but it was out of sight expensive).
Also, many memories of flying are just visceral, and I don’t really get that with the sim. Like the smell of avgas instantly brings memories of calm, cold, crisp, early mornings out on the tarmac doing pre-flight. And knowing, when the air feels like that, that its going to be smooth as glass up there.