Mental, your starting point is no doubt a good intuition but then the idea should not be stretched too much, otherwise I am afraid it becomes too simplified and loses its grasp on reality.
All designers (and all riders)
want a bike with as many advantages on the competition as possible. A very well balanced bike, like Yamaha, has
that as its advantage on other bikes that are less balanced.
"Taking the bike out of the rider's way" is a good reminder that the bike, as many advantages and qualities it may have, does not ride itself and has to be tuned to the rider. But that, I'm afraid, will have to be rider-specific. Taking the M1 out of Rossi's way may mean making it more powerful while preserving the handling; taking it out of "my" way would mean making it a 150 bhp bike with very smooth power delivery and super-easy handling
Honda have the opposite mantra, "take the rider out of the bike's way". For them the rider is the difficult-to-control variable. There are riders, like Stoner, who may be better suited to that approach and tend to adapt to whatever bike you give them. If you try to take the bike out of his way, he may not be able to tell you what to do...
He rides the thing to the limit no questions asked, and if he crashes he'll complain. Fantastic for the engineer to gather data -- that's why Honda want him. He's functional to their approach, whereas JB and Rossi were not. As you said, it will be super-interesting to see how Ducati (so far Honda-like) will be able to change their philosophy.