The Ducati that Stoner and the rest rode is far removed from the current bikes. It's not that Ducati got dramatically worse, it's that everyone got better. As the competition continued to evolve, Ducati was unable to keep the pace. Ducati sells bikes. It's all they do. They cannot compete with the funding Yam and Honda have poured into GP. When Honda will test 30 different frames in a year, you simply cannot compete. Honda is the worlds largest engine producer, and is involved in many race efforts (including Moto2 which is based around their CBR600RR engine). Those companies are selling dirt bikes, ATVs, watercraft, generators, lawnmowers and stuff. Heck, Yamaha is making pianos and keyboards. Ducati just makes bikes. Just look at any of the data. For example, I'll just pick a random race that Stoner dominated on during his championship year.
2007 at Misano Stoner set a pole with the Duc with a time of 1:33.918 and averaged a race pace 157.5 KPH which blew the competition away and gave him a victory by 4.8 seconds.
This past year in the Misano GP, the new Ducati ran an average race speed of 158.4 KPH by Dovi, and 158.3 by Hayden. The Ducs are still fast. But how about the competition?
In 2007, Stoner's best lap at that race was a 1:34.6. The best lap in 13? MM93 with a staggering 1:33.9.
If you look at stats across the board, you'll see that the Duc is not a terrible bike, but the M1 and the RC213V have just advanced much faster. Simply put, to expect Ducati to spend the type of money that Honda does in GP is unrealistic. I'm still a fan, but I have MUCH more hope about Ducati's production based efforts this year than I do about them advancing in GP.