Well from Yamaha's perspective, they could either go by results or by commercial value.
Rossi's massive fanbase and star power are substantial enough to provide him additional value over and above his race results.
And just as DORNA, Yamaha have placed all their eggs into a basket from which they may never be able to extract the egg without a significant financial cost and/or burden.
Rossi is far from stupid when it comes to business and IMO there is little doubt that he will licence his likeness and brand in such a way that any use of himself will result in financial reward to himself. Likewise, I would not trust Rossi to necessarily stay aligned to Yamaha in years ahead either as he knows his worth and knows that the Rossi brand transcends the manufacturer and in many ways the sport, thus he is in a more powerful situation than are all other riders and some manufacturers.
However, if we go purely by racing results, Lorenzo finished the 2014 season 32 pts behind Rossi and the 2015 season just 5 pts ahead (330 to 325).
Sure he (deservedly) got the title and bragging rights but for all intents and purposes they were nearly tied. Within the 'margin of luck' (if I may borrow & mangle 'margin of error' from statistics).
Nobody cares who finishes second in the world championships as there is no marketing or benefit to finishing second when you are on a factory bike. Sure some may argue that if you beat your team mate thence it gives you a leg up, but generally I would say BS when that team mate is the golden goose (that also applies to Marquez as I do not see Pedrosa getting benefit from HRC over Marquez)
So putting both factors together and one can see why Yamaha might value Rossi more.
The decision was made commercially thus the results have nought to do with it and it is all about marketing and the financial benefit of having the sports most popular rider in your team and colours.
When Rossi returned to Yamaha in 2013 he was unequivocally told that Lorenzo was their No.1 rider and would lead development. Two years on Rossi's performance had earned him the right to be treated at equivalence.
What Rossi was told and what happened could well be two totally different things
My opinion only but I do suspect that in 2013 Rossi started as number 2 to remove the expectation and pressures that would come with 'the return of the prodigal son', as after all, his Ducati years had started to raise questions and Yamaha did not want to go all out pushing him lest he fail and by extension, they fail him.
By late 2013 as it was evident that the old guy had lost nothing, he started to assert the power in the garage (again, this is due to the power he comes with because of his marketability and the power that is Jeremy Burgess) and I suspect that by season start 2014 he was easily on equal terms and personally.
I for one would not be surprised were he the one most listened to out of the team mates as afterall, he was allowed to sack his team engineer and rebuild the team he wanted/demanded despite the impeccable record of that team lead (admittedly there did seem to be a falling out and JB was happy to leave to be with his wife).
By 2016 there is little doubt to me that whilst Yamaha publically claim that both are on equal footing, the power is more on one side of the garage to the other which again was somewhat evident by the handling of season's end 2015.
Yes it may be true that contracts were offered at the same time, but in a savvy business world of dog eat dog, you can easily state that contracts were offered whilst at the same time making a resigning unpalatable to one (or both) knowing that if they go public they breach contract whilst knowing that in the longer run, public mutterings will come across as whinging. Yamaha were (IMO) brilliantly tough in the way that they handled the situation knowing the feelings of one of those involved and his concerns regarding lack of support from 2015
Point is, Lorenzo could have stayed at Yamaha and he would have been a title contender on it in 2017 & 2018. He chose to leave, perhaps because he felt a different manufacturer would value him more while still providing him with a competitive ride.
I do think it is all about Lorenzo feeling valued as he was shown a lack of support in the latter stages of 2015 and felt that he deserved better given his 3 from 6 championships although I am also not naive enough to believe that money may not have swayed him either.
Either way Yamaha's eggs are again in the one basket and as many have said it will be interesting to see the dichotomy of the team if/when Vinales starts to get competitive and then beat Rossi.