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From the point of view of my particular bias, that of being an even bigger stoner fan than most, I can find agreement with all three of J4rno, jumkie and stiefel in regard to race simulations..
Stiefel's post was a no-brainer for me, given dani's proven poor bounceability, doing race simulations with each lap running the risk of crashing is not something dani should do either to demonstrate or determine how tough he is .
With jorge and stoner, I would probably go with jumkie, different strokes for different folks. I also don't think jorge's camp, fantastic though he himself is, can be assumed to be dispassionate or agenda free as opposed to everyone else in motogp, or in the human race for that matter. His camp have been running this line for a while, going back to ramon forcada 2 years ago, that jorge is more virtuous/better because he is harder working than stoner. Forcada did have the perspective of having crewed for both of them, and it was hard to take too much offence as a stoner fan because he also said if stoner worked anything like as hard as jorge no-one including jorge would get anywhere near him.
This does not preclude the recent statement being self-serving, as stoner's claim for the aetiology for the arm-pump at qatar last year is quite different, ie dorna ....... up the honda bike by changing the weight leading to chatter.
As far as evidence goes, it is hard to see how jorge's race simulations have hindered him in any way, and certainly easy to argue they may help his demonstrably consistent performance. I don't see that stoner's method has cost him much though, and certainly not any championships. He didn't lose the 2012 championship because he finished 3rd at qatar, he lost because he crashed in practice at indy, and if he hadn't done that would have likely lost because he crashed in the second last corner at sachsenring, neither very likely to be related to insufficient race simulations. I think what has been said about his latter years at ducati is correct, he was always chasing and not always achieving a set-up, and I think he was more inclined towards race simulations in 2007 when finding a set-up was perhaps less problematic.
If jorge goes on to win further championships as seems likely, I think his method can be argued to be better validated than stoner's. In the interim, as others have said it is probably reasonable to look at what those who have had great success in the past have done. I actually don't know what doohan did, we didn't get great coverage in Australia then, but I don't recall rossi doing race simulations to the extent jorge does.