This article is really simplistic: Compare it to what Burgess says about this year chassis and you will understand a few things other than "the Honda is faster", especially after Crutchlow complained about having too much power during the same race. (!?!)
The Yamnaha have a longer swing Arm since 2011, it suits Lorenzo style (based on corner speed) better but since Rossi and Burgess started testing it, they figured a few things: It doesn't let them slide the bike during braking, so weight transfert canot be limited this way and they got less grip, it doesn't let them go deep on the breaks in the corner, and lately, Lorenzo complained it was too a"gressive" after the bike nearly spit him out on the gas in slipery condition, all of which is consistant of a longer wheelbase a weight distribution biased to the rear (comparatively).
Otherwise said, they lack traction or have too much of it depending on the part of the track and have too much weight on the rear wheel, making it harder to pass the power to the track and control slides (moment arm, leverage, weight), and to turn on the brakes as the Hondas does, you need a front which is planted, not the case here.
Not enough weight on the front wheel for controling its movements, also if the bike could slide more easily, they would find morergrip at the end of the race, as so far, they spend too much time where the tyre is at its maximum traction on corner speed, with bikes of this weight, they suffer more from the track abrasion than if the tyre was sliding earlier on the gas.
And it is not Rossi who was asked what he wanted by Yamaha since end 2010 but Lorenzo.