The problem is that Rossi, creditably competitive as he is at this stage of his career, doesn't have the pace to beat MM even on a flawed Honda if MM takes the decision not to throw his bike down the road, a lesson he learnt in 2015 and put into practice in 2016, with Valentino's superior points score in the last 9 races fairly irrelevant since MM in all reality won the title rather easily, riding conservatively until he clinched the title then throwing caution to the wind afterwards. Valentino also didn't have the pace at the end of the 2015 season to close out the title against Lorenzo in 2015 with MM out of contention.
Marquez is the best rider on the grid today, no two ways about that. In fact, had he ridden sensibly in 2015, he might have contested the title against Lorenzo.
My point, however, was that the Yamaha's results did not, in fact, deteriorate over the latter half of the season. At least for Rossi.
Lorenzo on the other hand has shown the ability to be faster than everyone, even MM, on a Yamaha shod with tyres that suit him. I still think Yamaha's best chance was to back Jorge and lobby for high edge grip tyres. Perhaps Vinales will prove up to the challenge, but like others I am not as yet convinced he has the race craft or is able to sustain his pace through a whole race with sufficient consistency.
That's also a gamble in many ways. Superb as he is when the setup, tyres and conditions are good, Lorenzo might end up at the other extreme when the situation calls on him to ride around the problem (ref: FP3 Phillip Island 2016; 21st place behind Rabat).
There's no point finishing 15 seconds ahead of Marquez in one race, only to finish 5 places behind in the next one.
Still, Yamaha
did put the 'best' contract he'd ever been offered on the table, he felt it was time for a change of scenery and assumed (not unreasonably) that he could contend for the championship on a steadily improving Ducati, a bike that had registered 8 podiums the year before, and almost registered a 2-3 finish at Qatar, all under riders who were good but well short of alien material.
Wasn't much Yamaha could do about that. Though given Vinales' long term prospects, it seems to have worked out quite well for them.
All of these multiple championship guys ride to win championships and then races anyway, with no-one remembering who got 2nd rather than 3rd. Do you think Valentino cared about Pedrosa relegating him to 3rd in 2007? He was working towards winning the 2008 title, pushing Yamaha in regard to their 2008 engine, no matter whether early versions of that engine blew up or ran out of fuel initially in the late races of 2007 after the championship was decided.
Rossi may not have cared in 2007 but I'd say Lorenzo definitely cared in 2016.
More importantly, if Marquez has a 2014-like season, neither Rossi, nor Lorenzo would have a chance. But Marquez isn't a sure thing - he was too close to disaster several times in the season and his pts cushion at the end wasn't really large enough to accomodate more than one major mishap.
And if something like that happened in 2017, a rider like Rossi who could be relied upon to be not just consistent but fast in all conditions & on all tyre types would be a stronger bet to capitalise on the situation. On Bridgestones, he finished just 5 pts behind Lorenzo. On Michelins, if not for the Mugello incident, he'd have finished 46 pts ahead.