It's pretty common knowledge that Honda had big problems with the handling of their bike into 2010. They brought a low-loader full of frames and swing arms to Qatar and made Pedrosa test them all, because they were fed up with him just saying.." I don't like it and prefer the old one"
Personally, I think Dovizioso's efforts to sort that bike are underestimated. He was the muel racing with new stuff and was hot from the start of 2010. Pedrosa had a good run through the mid-season then got injured and Jorge ran away with it.
Honda threw everything at the bike 2011 and it was head and shoulders above the Yamaha, who didn't really make any progress until 2012 and the new class. Why change a proven championship winning 800 formula that was gonna change the following year? They tried to make what they had last as it was 2011, the last season of 800. Their development program was concentrated on the 1000cc bike.
Sure the Japs got caught on the hop 2007 which is why Stoner won. They caught up with pneumatic valves 2008, but the big step was getting the Bridgestone tyre 2009.
Stoner winning pressure free races at the end of 2010, by reverting to his shit or bust method, does not constitute a competitive championship contending bike. It just shows that he had to ride the bike beyond it's limits. You don't win championships pushing at 110%, as he illustrated. He had a different agenda at that point and it wasn't riding for a title.
Rossi's agenda was different. He wasn't interested in employing the same win or bin method to mount a title challenge. Breaking his neck to mask Ducati's engineering woes was not part of the plan. He told them that and gave them new direction but they we too slow on the uptake. The bike DID improve as Hayden says, just not as fast as the others through 2011 & 2012 which has been the big step up period for the Japs.
First with Honda, then Yamaha and from mid 2012, Honda again. Ducati doing fuck all over the winter and likely as not starting Qatar with the bike they finished with at Valencia will mean the gap to their MSMA competition grows again, while The ART bikes get closer to them.