I'd posit those who are saying Yamaha made the right choice in keeping Rossi based upon the two consecutive 2nd place title finishes in the last 2 years, don't really know their ... from a hole in the ground if they actually believe that is a good reason. Last year would have been an easy 3rd had MM not done Yamaha a favor and crashed out numerous times before settling down far too late in the season.
As has been pointed out by Jum, myself, and others, being given a M1 or RCV assured you no worst than a 4th place finish in the championship. Over the past several years. 2016 might see this change, but as Honda and Yamaha's legion of computer techs come to grips with the Magneti Marelli ECU, this will be the same in the 2nd half of the season most likely. The Suzuki/Ducati threat is not going to last the full season.
Rossi's 2nd place title finishes appear impressive on the surface till you consider no one outside of Yamaha and Honda have any real chance.
There's enough talent in GP to replace Rossi now, and replacing him with oh say, Vinales for '17 would be a wise move.