You end up with buttons that are way to large to allow for finger taps that make no sense with a mouse, so a lot of wasted space.
Forcing stupid gestures and UI animations that make zero sense with a keyboard and mouse.
And of course, the fact that you have legacy applications that will never be updated to fully support it (and likely even new ones) and the experience will never be great.
A single device that is meant to be fully usable with a k/m and touch screen is always going to be a compromise for one (or both) setups. At least iPad OS while you can attach a k/m (with decent results if really not how it was designed to be used) the OS is clearly touch first.
I doubt we are ever going to truly see an OS that can handle both with the respect that each input method deserves. The only way I really see that possible is if the OS forces every application to use built in libraries for navigation, buttons, etc (and I mean force!, like it would not run if you don't use it) and the OS then shifts between the 2. But even then you could not naturally switch between, oh I am typing but let me just press this button on the screen because the OS would be on a specific mode.
Its easy to say that Apple just wants to sell us another device, but let's not forget that Microsoft tried and failed... horribly... And we still see the problems with this idea in Windows 11.