I think the answer is pretty simple really. To me it's the tyres. As Jum bought up once or twice, tyres are the most crucial thing to a rider, moreso than the bike itself. Stoner proved a tyre & rider can overcome a mediocre bike when bridgestone developed a tyre to suit the Ducati. As soon as his preference was removed from the allotment, he went from looking like a riding god, to looking like a rider who saw god when the Ducati tried to kill him.
Vinales ended at Suzuki and started at Yamaha with a tyre he was comfortable with, and his results justifiably had him as a contender. Early in the 2017 season, the ........ rider vote ordered by Dorna on behalf of Rossi, resulted in his tyre preference being removed from the allocation available and his results suffered from that moment on. I'm sorry Mav, but your prefered tyre is unavailable as of now, we all agreed you can't have it. Try this one, we all think it's better than the other one. Thanks.
While I'm not putting Vinales in Stoners company as a rider, I see directly comparible results when their prefered tyre was removed from the available allotment. Both were pretty dominant at the time up until there tyre was removed, then results went south dramatically in comparison. Rossi proved how crucial tyres were when he threw Michelin under the bus in preference to Bridgestone in 2008, then went and beat Stoner to the Championship. Stoner lost his prefered tyre, and Rossi gained a tyre he prefered, and the championship went accordingly.
Pretty simple IMO. IT'S THE TYRES.