I didn't have a hard of a time getting used to the mechanics of the Steam controller, but I think that might be because I use gamepads extremely rarely. I would think retraining muscle memory would be harder when you're using a controller that is 90% similar but behaves in different ways than coming from something entirely different like M&K.
That's not to say the Steam controller was quick to get into, though. It takes a hell of a lot of tweaking to get to feel "right" for me, but if I can be arsed to do it I have a pretty good experience with it. Oftentimes I can't be arsed to do it, though.