I also agree with you that X-Plane still gets an edge in terms of flight model, even though the gap is not as wide as it used to be between X-Plane and FSX/P3D.
The one obvious shortcoming of X-Plane, when compared to MSFS, is the lack of accurate world scenery, on the one hand we could say that it's just eye candy but on the other hand accurate scenery could help students prepare for VFR flights. Yes, you can generate high detail scenery for X-Plane using Ortho4XP, but it's time consuming and it requires a lot of disk space.