I don't think there was too much wrong with the 2009 bike, in the hands of a healthy stoner anyway. He repeatedly said the problem was with him, not the bike, which I think was championship capable had he been fit the whole year. He basically had no dnfs, depending on how the warm-up lap incident is classified, which was more of a dns.
Something was drastically wrong with the 2010 bike even in his hands; sure the tyres may have contributed, but they changed many things, including going to a bigbang engine, in the search for "general rideability".It still remains so that the bike was not reliably ridden, whatever the tyres, at front of the field pace except by stoner, and it is also true that no-one including rossi has been able to duplicate his method of riding it. Interestingly on another forum recently there was a quote from troy bayliss, and he said he could not duplicate stoner's riding method on the ducati 800 either; he also said it was very different in character to the gp06 on which he won the race.