Rossi (and now Lorenzo) have always been complaining, each year, about the (relative) lack of power of the M1. Lorenzo was still complaining during the recent tests. Maybe you should ask them if there is a problem or not there.
The front section of the Yamaha is not wider than others, in spite of it being a IL4. They have managed to reduce the space between the cylinders to a minimum (and had to solve serious overheating problems in the process).
Your last comment about the 2-strokes and Rossi: Rossi rode the 500s when he was young, after that he has had many years with completely different bikes, of which the last seven years with the supersmooth M1. So age and habit are a factor there, but give him some more time... It's early to rush to
such conclusions...