Every great team and rider can have a bad year. I wouldn't be so harsh on Rossi and Ducati.
The big problem is, of course, Honda has awaken for its years long slumber. Nobody, not even Yamaha, can spend as much as they can. No other motorcycle manufacturer has their expertise and human resources (yes, they often fail to apply them to road bikes but that's another matter we already amply discussed). Once they got the HRC leadership together and finally accepted they needed a great pilot to win, they were back where they belonged.
I wouldn't still count Rossi out but the Honda we are seeing today is a much more formidable opponent of the Honda we saw around 2007 and 2008.
Ducati has the racing expertise, a large sports budget but it cannot realistically hope to win against Honda in a straight spending war, especially if Honda is able to retain the services of Mr Stoner. If rules become tighter, it will be worse for them since performance improvements will become much, much more expensive. That's why they are generally opposed to restrictions.
Save your scorn for Ezpeleta and his wacky CRT idea. Colin Edwards set a goal of bringing the the Suter-BMW to 2,2 seconds in these Sepang tests. He managed a 4,2 gap by riding the wheels off his machine. The FTR framed bikes proved to be not only embarrassingly slow, but also quite unreliable. No wonder they removed the 107% rule and gave them 12 engines for the whole season...