I will agree with you that the 4 Honda/Yamaha factory rides will give anyone on the grid a significant boost. The problem is they still have to ride it. Marc is a perfect example of this. He has one of the best 4 bikes on the grid, but can't finish a race because he refuses to change at all. Ben Spies is another example of a factory rider not getting it done on raceday. Rossi went from a championship bike, to the Ducati and .... the bed, back to winning and lots of podiums (and several 4ths) on M1 again. Same thing with the current Ducati riders.
Rossi is a tactician. He's not as fast at Lorenzo or Marc, but he's gotten wiser over the years and seems to be able to run "his" race opposed to trying to run the blistering pace everyone else does. Argentina was a good example of this. Misano is another great example. I don't think he was baiting Lorenzo into doing what he did, but was just tying to make sure they were close. When I saw him go down I just assumed that Marc accidentally grabbed Jorge's bike. Minimize the damage he would have done to the point lead.
So I will agree with you to an extent, not that you pointed out anything mind warping. This has been the case for years, minus a few dark horses we cannot mention. F1 is far, far, far worse in terms of viewing and favoritism than MGP.
And Jum, don't be such a close-minded American. Over the pond it's a Coventry Steamer
There was this bloke called Max Biaggi, who did seem to be fairly good, who thought he just needed to change marques to win a world title.
Sure you need a factory Honda or Yamaha to win a world championship (except for that one year I won't mention), but whilst there are perhaps some riders who never get the chance to demonstrate what they really have, I don't believe just anyone can win a world championship on one of those bikes either.