There is a minor issue where the game often displays the wrong input instruction (e.g. "press Y" instead of "press A").

A bigger problem is that, if playing in gaming mode, you have to manually scroll through several dozen action sets if you want to customize the controls for any game (most of the games have their own set), which is a very slow process on the Deck. What's supposed to happen is that the correct action set is opened for you automatically, but that is not currently supported in the new Big Picture interface.

So until that's fixed, expect to spend a lot of time scrolling through these to do things like raise trackpad sensitivity, which is very low by default. Or you can play in Desktop mode until you have all the controls configured how you want them.