Trouble was the competition moved on at such a pace a small firm like ducati did not have the resources to really further the project from the 07 800 inception bike. This started to show with casey in the years after 07 on the duc and has continued on the downward spiral since. You can work your balls off making a bike faster and spend stupid money but if the competition is moving forward faster it looks like your going backwards.
I would be interested in knowing what ducati lap times were in 07 compared to 2011 on the same track with similar weather conditions same as for the Yamaha and Honda? My bet is the bike is faster, just not to the same progression as the competitors.
I think that is more a case of Ducati saying the bike is fine when it clearly wasn't. If they were prepared to listen to the riders & try to engineer solutions from when the 800's were implemented, I think they would be a lot further ahead of where they have ended up.