They certainly did have a more powerful engine that year, particularly compared with the spring valve Yamaha, the desmo valve Ducati I understand having an efficiency advantage in what was essentially a fuel economy formula. Honda didn't have much to complain about as I gather it was they who basically provided the major impetus for the new formula.
Ducati were also purported to have such a major electronics advantage that the bike rode itself, which was far from the case, the electronics I suspect merely converting a bike that was completely unrideable to one which was almost unrideable. The initial iteration of the GP08 with the new 2008 engine was pretty much completely unrideable even for Stoner on the tighter European tracks, and they had to revert to the 2007 engine if you recall, although Stoner also had an early season DNF due to an engine letting go. I remember Nicky saying when he first got on the GP08 at the post-season test that however much Ducati were paying Stoner it wasn't enough.
They are not such an underdog now with the German money, but as I said I don't think they deserved to be chided for looking for innovative solutions when they were an artisanal operation as was the case for much of their tenure in motogp. Certainly they started from scratch with Bridgestone when Michelins were the go if you were in the top tier of the teams/riders supplied by Michelin, but were only allowed to run with the tire co-developed completely within the rules and spirit of the sport, which was closer to a prototype series back then, for 1 year after achieving parity or better with Michelin in 2007 following the demise of SNS tires at the end of the 2006 season, the control tire being more or less the consequence of that bolt from the blue 2007 title win.
