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Well, for starters, this of course:
"I'm not a Stoner's fan"
No, seriously though, I wouldn't say you went in a wrong direction, I'm no expert on the matter myself to begin with, and solving the Ducati's problems has been too great a challenge even for people that are. So it's all just a matter of different opinion.
I think you are dead on right in your analysis of the Japaneses companies' success, in short evolution rather than revolution and capitalizing on strenghts. But I'm not sure Ducati should follow the same tactic at this point in time. Since entering motogp, Ducati have always been about fast technological innovation and a thinking-outside-the-box approach. Quite often, this way of doing things has actually worked in their favor (2006, 2007, 2008 were great seasons for them). They outsmarted the Jap's at least once, and the whole story of the Ducati motogp project up to 2008/2009 should be considered an immense success.
As it is now, the have a motorcycle that was hastily developed to mimic the standard engineering solutions of Honda and Yamaha. Evolutionary change might see them behind the eightball for a long time.
However, there was a time when I believe that would have been the best approach for them: when they introduced the carbon fibre frame. I believe they should have stuck with it and gradually perfected it. A gamble perhaps, but one that may have very well paid off in the long run.