Wosi I deliberately referred to Qatar 2009 precisely because Stoner crashed in 2010 (on a bike which had become unstable after ducati had made a decision to develop the bike away from him in search of "more general rideability), although you were selectively referring to rossi's fastest lap times rather than his race times for your own purposes. Both Stoner's fastest lap and finishing time in 2009 were faster than rossi's in winning the 2010 race on the bike which won the championship that year, or when he finished 7th in 2011. The comparison most likely to be even, the 2010 post season test which was only 2 days after the race and which had the internal control of stoner's performance on the honda in testing vs pedrosa's in the race also tells a story which you have never addressed.There are also statements by many people who have ridden/been involved with the ducati including rossi himself that stoner did something unique to make the thing go so fast which it is basically impossible for others to replicate.
Without necessarily any implications for their overall quality as riders (rossi obviously has to be rated well ahead of stoner overall), stoner was patently better at riding the deeply flawed ducati 800 bike, and deserves praise rather than all the condemnation he received for his performances on and "lack of development" of the thing, which as you correctly say is the reason for current criticism by some of rossi, tedious though that has become. Stoner it would seem was able to extract something because of unique elements in his riding style, as somebody said quite possibly at significant cost to himself, I don't think even he enjoyed riding the thing.
On the other hand, if you were to design a bike to be peculiarly unsuited to valentino, the ducati would meet every criterion. When not in a slanging match I would concede this makes the design of the bike deeply flawed rather than proving any deficiency in valentino. Even so, I don't see how stoner can be blamed for anything to do with the ducati, other than that by his ability to ride around the flaws of the bike he made everyone including ducati corse, general ducati management, ducati's sponsors, and even jb and valentino think the bike was much better than it actually was.
I am not even sure about the whole tyre narrative, stoner never complained about the tyres while he was at ducati and has not really done so (concerning the time he was at ducati) subsequently. It would seem reasonable to assume that the tyre he had in 2007, with which the bike was co-developed, suited the bike in the same way that the sns tires were purpose made to suit the bike and the prevailing conditions. Other than the 2 races post laguna seca in 2008,where other explanations could possibly apply ( and in fact were applied) the bike was not unstable/prone to letting go without warning prior to being revamped for 2010, and stoner at the time anyway said that the 2009 bike was fine and the problem in that year was with him, specifically his health, with which observed events would seem consistent.
So the bottom line for me is that rossi deserves all praise for his glittering career which is not diminished by 2 years on that pig of a bike, you have a good case for blaming ducati all you like, but disparaging what stoner did on the thing is unreasonable imo, particularly since such disparagement preceded and largely provoked the current admittedly unjustifiable criticism of rossi, as you yourself say.