Honestly? Everything.

X-Plane actually models the airflow over wings, fuselage, etc (simplified, of course!)
Basically, the difference is MSFS reads a table with speed, aoa, etc to see how a plane flies. X-Plane actually models the physics.
This is especially nice for situations like stalls, especially with any sideslip, where the situation just can't be represented by a table!
It also models propwash and jet blast, and these can interact with the flying surfaces of the aircraft as well.
By the way if you're interested in seaplanes, the water dynamics are amazing and very realistic; (I'm a licensed floatplane pilot) It's a lot harder than it looks!
This is a (very long!) article on the X-Plane 12 flight model by Austin Meyer, the creator of X-Plane. No need to read it all, but there's a lot of good stuff in there!
https://developer.x-plane.com/article/x-plane-12-flight-model-report/