Lorenzo has had the upper hand this year no doubt. From Rossiīs point of view, I think it looks a lot like another problematic year, 2007, when Stoner beat everybody (except this time he got beaten by his "teammate" on the same bike - and in 07 Rossiīs problems were more related to the bike & equipment, not health).
Three years ago there was a lot of similar talk, that now Rossi is getting too old, and Stonerīs the īreal dealī (not denying that in a way he is, of course!).... but in the 3 seasons, that have passed, Rossi has taken 2 world titles, Stoner hasnt, and Rossi now holds a narrow lead on Stoner going into the last round.
So, it looks like Stoner only had that one very succesful season (not saying he canīt or wonīt repeat it as early as next year). Remains to be seen, if Lorenzo will do a better job defending his title.
All in all I think one of the most important signs of a great champion is the will and ability to rise back to the top after troubled times.