Thing was, back in 2007, when he won his World Title on the Ducati, it was the best bike. That engine was just so much better than everyone else's that he could run away from them. I can't remember exactly, but I think it was the year before or early 2007 that Capirossi was in the running to win the Championship on it, but he had a major accident when someone got slightly ahead of him at the start of a race [maybe Jerez..? Dunno.] and he came up side-by-side and the other rider's handlebar jammed on his front brake. Considering that you only have to caress a carbon brake to get it to stop, Capirossi went over the top and injured himself badly. His accident is the reason why they have brake lever protectors these days, by the way, and it put an end to his competitiveness at the time.
Thereafter, the other factory bikes just gradually overtook Ducati. During 2006-07, Yamaha had been having troubles getting theri pneumatic valve system running reliably enough on the M1, which put paid to Rossi having a chance of winning championships in those years, and Honda were just developing as they always do. Nicky got his 2006 World title by just being consistent and reliable, and Hondas are always that, even when they're not the fastest.
Don't get me wrong, I was a fan of Casey when other people weren't. I just think his efforts weren't as superhuman as some people like to think. However, on his day, he could make slower machinery go faster than it had ever gone before, there's absolutely no doubt about that.
