There is many ways to look at things...
I for one say it is an equal pairing of Rider and Machine.... unless of course you have the best bike on the grid and have custom tires made for you for each race (Rossi the not so GOAT). Dovi has obviously stepped up his riding this past season, and I think Stoner has quite a bit to do with it, mentoring him and also in the development of the bike.
if Rhea stayed with Honda, Chaz would have now had 2 or 3 titles, instead of zero. but he didn't and will take 2018 WSBK.
If Lorenzo stayed with Yamaha he would of been fighting for the title this year if not won, but he went Ducati and now sucks.
Marquez, can ride anything I think... But he lacks the ability to build a bike or so it appears.
Stoner, could ride anything & perhaps give that development advice which has helped Ducati this past season?
So many variables to the game, but I would say adaptability as a rider, and a package that can meet the needs of a rider and give them the confidence to press harder is what will win. just like Marquez shows every weekend, crash or win.