I don't have any experience with Godot. But given a choice between GameMaker: Studio and Unity3D for 2D, I choose the former. And it's because of the tooling. I don't consider Unity3D's tooling to be great for 2D. I don't consider it poor, either. But I think in making a good engine that offers 2D and 3D, some of the workflow is suboptimal if you're only working with 2D. That said, I've used Unity3D lately even for 2D projects, because my collaborators have been more familiar with it.