Great thoughts. Finding that balance is definitely tricky. Certain aspects of defining motion work really well with direct manipulation (state/layout, "tweaking" things, working with transitional/discrete animations), while others don't (complex state logic, event-based motion, generative animation effects). I'm really excited that there's such a focus around this topic in our field. It has really benefitted other design disciplines.
Personally I think that in order to be flexible and creative enough you can't really get around learning some sort of programming language for your prototypes.
In principle, I agree with the post and have felt for a while that motion was written off by a lot of designers (not like they were necessarily wrong).
That being said, with Material Design, I feel like Google is towing the line very closely and some animations bordered went beyond providing meaning into the territory of ornamental flourish.
A lot of animation and motion effects are great for the first time experience, but can quickly be detracting from the experience (one example I can think of is the transition for opening folders in the first iOS7 release). From the demos I watched, it really seemed like half the motion was really valuable, and another chunk wasn't. I'm eager to try a device out to see how it is in practice.
Great post ! Seems like the war is now Prototypes Tools VS After Effects ... This is by far the best way to communicate IxD and inspire your team to seek perfection while building the product through your vision.