I don't detract from Rossi's prowess in his heyday, he may even have been at least MM's equal as a 25 year old himself. It can never be known, but my gut feeling is that peak MM (if he is there yet) has a little more raw pace than peak Valentino, but VR might have got him on tactics/strategy and development/set-up ability, although we don't have much evidence that recent or even close to peak Rossi stands up well in a close title battle.
It is indeed creditable that a late 30s Rossi is so close to being competitive with MM, but MM being at his peak and so good is my whole point; even with the 2015 Yamaha possibly being the better bike, Yamaha won only because MM wouldn't settle for achieving anything other than a win in a given race. I believe the numbers say if he had accepted the positions from which he crashed out he would have won the 2015 title. So Valentino to win the "precious"/glorious 8th/10th needs both HRC to come up with a dud bike and MM to race injudiciously for a whole season again and possibly an unusual number of wet races as occurred in 2015, with the added problem of riders of bikes other than factory Hondas and Yamahas possibly being in contention for the title.
The arrogant Honda engineering culture can always come up with retrograde 'improvements' for the Honda, and MM hasn't demonstrated the ability of Doohan and possibly Rossi to influence them away from the wrong path. However while MM admittedly just nearly threw his bike down the road unnecessarily with the title still in play, I wouldn't count on him doing so if Rossi was the other contender.
So what we have is Rossi at age 38 being the Yamaha factory's focus rather than someone younger and possibly faster in the other seat, and Pedrosa being basically a contracted wing man, which to me means more MM titles unless Ducati can catch lightning in a bottle again or KTM advance their bike rapidly.
Hence as I have posted previously imo Rossi, great though his past achievements may have been, is holding the sport in general and Yamaha in particular to ransom in pursuit of a 10th title he never needed anyway. Again imo, Yamaha would be better/would have been better backing a younger rider who might have the raw pace to compete with MM, pace which both Lorenzo and Vinales showed they potentially have/had although perhaps only in limited circumstances. The tyre situation is a case in point; surely Yamaha in terms of title chances would be better pushing for a tyre which suited Vinales, and would have been better backing Lorenzo and pushing for a tyre of his preference, given tyres which suit Valentino suit MM just as well or better as the most recent season demonstrated.