As far as I'm concerned, the BIG fight between a recovered Rossi/Yamaha/Michelin and Stoner/Ducati/Bridgestone didn't happen in Estoril. Stoner had some clutch issue, and if you look at his times during the race, he wasn't lying. Actually, he lost quite a few 1/10 of sec around lap 5, when the problem started, then had a big dip a few laps later, but later on his times were very close if not parallel to Rossi's and Pedrosa's.
I think that he would have fight for the win if the clutch issue didn't come about.
Now, let's see what happens in Motegi where Ducati (and the 990) has won for the last two years...