There has been a bit of confusion surrounding certain aspects of Super Mario 3D All-Stars. Thankfully Nintendo has stepped in to clear things up.
First off, when it comes to Super Mario 3D All-Stars itself, Nintendo has confirmed that the game does support the Pro Controller. You can enjoy all three games in the collection with the Pro Controller, so no worries there.
Moving on to Super Mario Galaxy specifically, the official website for the game mentions that motion controls are optional. Nintendo has clarified a bit by saying that if you want to use the pointer functionality, you'll have to use motion controls. That's for docked use obviously. If you're playing in handheld mode, pointer functionality has been remapped to the touchscreen.