Issue not necessarily appearing on the Steam Deck but it would benefit from it as well - better handling of mixed input from a controller and mouse. I have a Steam Controller and prefer to have it simulate a controller in FPS games but to have the right touchpad work as a virtual mouse to ignore in-game acceleration curves and deadzones.

Some games handle it well, like Cyberpunk 2077, some games like Grounded tend to show keyboard prompts whenever it would detect mouse input but still function correctly. If I’m not mistaken Borderlands 2 would drop it’s UI controller layout whenever a mouse input was detected, which can probably be skipped by using layout switching/overrides from Steam Input. The worst offender so far is Hunt Showdown, where the game freezes for 0.5 s when it detects mouse input, even if it’s a physical mouse input.

All of my testing has been conducted on Linux, not sure how it behaves on Windows