I dont think the Honda is really that bad. Histoey tells us that plenty guys who didnt have the "best" bike out there have won the championship. And not just in GP. The great riders ride around the problems, and win in spite of these things. The Honda isnt the best out there, but, racing is about who can get the bike set up best, and how they overcome problems.
Pedrosa is getting the best from the Honda, and lets be honest, what works for a wee guy like him, isnt going to work for Hayden or others. Maybe I'm cynical, but HRC havent built a pup in a long time, so I think that once the other guys get it working for them, we should see more Hondas at the front.
Personally, I think a lot of the problems are down to riders not getting a handle on the bike quick enough. As Sheene once said of another rider "He couldnt develop a cold, never mind a motorcycle."
I dont see the Honda guys having a regular GP winner (historically) between them, I don't think that helps.
Pete