I think it's a combination of all those factors. Also, the M1 may not be that slow of a bike. It might just be that the Honda is that far ahead of everyone else. I've read about the advantage that Honda Transmission has over Yamaha's, which leads to less fuel consumption, better corner entry and stability through turns, and better drive out of the corner. Also, the well publicized fuel restrictions are a huge factor. While it has certainly impacted everyone, Honda adjusted the best. I remember Rossi saying it felt like the engine had no power, like it was running on air alone. Then you have a rider in Marquez who is on top of his game, and can exploit all these advantages to the max.