I’m willing to bet that most games that use mouse mode will have to use the face buttons and control stick on the mouse con. Metroid prime 4 apparently does this. So its not replacable with a standard mouse.

I think the joy con can also sense rotation of the mouse which is used in mario party and probably never again like the ir sensor from switch 1 joycons. I guess a hypothetical 3d mario maker could let you rotate blocks with it, but that could be done in many other ways.