For example, I explicitly stopped using a supposedly more realistic yoke controller in favor of a HOTAS joystick because I repeatedly found that I just _can't_ translate the physical inputs to a real plane. Yoke controllers in particular seem hard to get right (or maybe mine is just bad), but more generally, PC controller axes have a surprisingly low resolution (just 256 steps on an axis) making them wildly less precise than real thing, plus there's no force feedback. Using a completely different (and more precise) type of controller seems to help keep my brain from drawing conclusions it shouldn't.
Simulators _do_ seem helpful for more abstract stuff, like going through checklists, practicing maneuvers, experimenting... so long as you're very intentional about what you're trying to learn. I think I benefited some from practicing ground reference maneuvers [0] in X-Plane with a VR headset, for example, since they're largely visual and aren't tightly tied to physical inputs. On the other hand, practicing stalls in the simulator has probably lost me a decent amount of time in the air with my CFI trying to un-learn the wrong ideas I picked up, due to both control differences and (I think) simulation differences.
[0] https://www.faa.gov/regulations_policies/handbooks_manuals/a...