Unfortunately Rossi's been left to fix the mess Stoner left behind
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At the moment on a quick count yamaha have won 15 riders championships and honda 14, and ducati, currently making their 19th attempt, have won one. However your argument seems to be that the one win was entirely due to the bike, whilst the subsequent seasons were aberrations and the fault of the rider who won the single championship. There are those who might suspect some prejudice in this position, at least unless and until valentino actually wins a championship on a ducati.
As I have said previously I think rossi is the best developer in history, but I doubt honda, stoner or fans of both or either will care about how well valentino is developing the ducati as long as stoner keeps winning races and (hopefully) championships.
As another point the strength of hypotheses (or assertions which see to be your stock in trade) depends on the ability to be consistent with future events. Since you have only been on the forum for a few months this cannot really apply to you, but I among others in 2007 said that stoner had a narrow window to win another championship with ducati (basically 2008, in which the bike at least from mid-season was good enough), because of the superior engineering and other resources of honda and yamaha, and would need to move to another team, preferably honda, to win more championships after that. I also said prior to this season that if rossi could not solve the front-end instability problems of the current ducati design he would finish with more points than stoner did in 2010 because of their different approach, or rossi's superior tactical/strategic ability or intellect if you like, but would challenge less often for wins and podiums.
A further point is that ducati deliberately decided to develop away from stoner for 2010, whether because they saw him as unreliable or likely to be leaving, or because they anticipated valentino's advent, and it was the 2010 bike rather than the 2008 and 2009 bikes that had the front end instability problems which persist.