I think the difference is that 3D is inherently continuous (because it is simulating a 3d space) and requires another layer of abstraction on top of the controllers to work intuitively. 2D on the other hand is pixel based which is usually discrete (the world units are uniform in pixels), and also the character movement is 1:1 mapping on the controller. These two factors make 2D feel more responsive, and I'm guessing that once VR gets better it will close the abstraction gap and make the controller mapping (body/hand movement) 1:1.