I agree that CS can absolutely retain his title, though there are some that would like that question phrased as: "The bike looks to be back to its best now, so does he have what it takes to win it again?"
And that's not fair to rider nor bike. Motorsports have had countless 'fit-like-a-glove' partnerships. Usually, the talent has already shown success elsewhere, as in the case of Fangio, Senna, Roberts Sr. While Stoner did have some success in 125s and 250s, he was not dominant in MotoGP until he joined Ducati. It's the extent of this domination that makes folks point directly and only to the machinery as the source of his success.
However, it may just be a perfect match between rider and bike. The fact that others can't ride it equally as well should be seen as a separate issue.
If I had a few wishes to cash in, I'd like to see Rossi and Stoner ride each other's bike with each other's setup. Then, let Rossi adjust the Duc and Stoner adjust the Yamaha and try it again. That would be fun.
Sorry for going off topic there.