What's going on at Yahama revolves around a lot more than Lorenzo integrity.
Especially since his 2012 talks with Honda.
He had the design team wrapped around his little finger for 3 years, they neglected the second pilot for two of them, couldn't ignore Rossi and even Less his technical insight last season since he is by far the best they had since K.R for set up and development.
From Yamaha staff comments, their experience from 2011 and the need they had to revert to the 2010 bike parts and base set up in 2011 and 2013, the loss of both championship last season, the uncompetitiveness of their second riders is not what interrests them.
They want a bike that doesn't loose to the RC in most tracks, can take points of them even ridden by satellite riders, and allows for their No2 to be competitive, this was not possible with the "Lorenzo way", as simple as that.
He has his agenda, he spoke to Honda in 2012 they didn't like it (nor did they like Rossi deserting to Ducati), but they can't afford loosing to Honda the way they do it because it doesn't matter how many races Lorenzo wins, if the factory looses titles it's what goes down the record book.
Something else, Honda is not going to make a 250 style RC for him, if he goes to Honda they will bend backward to suit him but already said this winter they couldn't make a Yamaha, they tried to increase corner speed with the RC, they failed.
I don't know enough of Ducati to say anything about it but in Yamaha case it's clear they look at the factory best interests and Honda are not Santa Claus...