The tyre advantage was gifted to Bridgestone via a regulation we must remember, a regulation which completely negated Michelins supply strategy, which was in essence the ultimate in prototype development across a race weekend.
This reg combined with the fuel limit IMO are the two biggest contributors to the escalation in cost. People love to blame Rossi for the control tyre, but it was the MSMA who are directly responsible, with less influence by rubber the focus has shifted to bike engineering and software, playing directly into the hands of Honda and making the sport ridiculously and prohibitively expensive. And funnily enough at the time the tyre supply reg was implemented to reduce costs.........an overnight special somehow seems quite cheap now.
As lex has pointed out this plus the rest of regs post 2007 could have been Hondas way of stopping burgess and Rossi, what it has done is made the audience question what they are seeing and turn away through boredom and predictability, not too mention questioning the reasons that have been given for the regs which, for me are right up there with the WOMD excuse. With the MSMA influence now limited let's hope Dorna can find a decent solution, at the moment it still seems unlikely.
Honda undoubtedly bear large responsibility for the unsustainable cost structure and recent (and possibly current) one line nature of the racing consequent particularly on the fuel limit which they appear to particularly champion.
I think it is rather a stretch to hold them responsible for the demise of the overnight tyre rule given that michelin were their tyre supplier, or for the control tyre as they seemed happy to stick with michelin and give them time to come good. The latter was substantially contributed to by 2 riders, valentino and dani pedrosa, particularly the latter, for reasons of short term self interest, understandable though those reasons were from the perspective of a rider wanting to win a particular championship. To be fair I am sure Michelin's financial woes which preceded the gfc didn't help their motogp race tyre program in 2007 and 2008. I also think the overnight specials were becoming too expensive for them to sustain anyway.