My theory....
Theory only...thought I'd throw a conspiracy out there seen as there have been a few floating around this season.
This season has been scripted from the beginning...Mercedes agree to let Rosberg win the championship only if he retires at the end of the season...a German wins in a German car.
However, Hamilton is not initially involved with this agreement for obvious reasons.
Hamilton experiences 2x poor starts, 2x mechanical issues and then the silver arrow smash in Spain...he threatens to quit (
http://www.skysports.com/f1/news/24...eaten-to-quit-mercedes-after-spanish-gp-crash).
It is broken to him then, that this Rosberg Championship deal has been brokered and that he is to toe the line, he will get his chance again after Rosberg leaves.
Then as the season progress' it is scripted to make it look like Hamilton is 'just having a bad day at the office' in terms of reliability. Capping it off with a brand new engine blowing up in Malaysia, the final nail in his championship bid.
Hamilton can't rock the boat fully, as he knows he still has a future with the team...tens of millions still to be made and maybe a few more championships before he retires but still has to have the odd dig, and 'moan' about the issues with reliability.
Then comes the final race. By this point Mercedes have won the Constructor Championship by miles and Rosberg is Champion if he comes at least 4th or above, if Hamilton wins.
Hamilton knows this, and has the almost perfect tactic, slow down in the slow section and push Rosberg back into the Ferraris/Red Bulls. He cannot do this straight away, because he has been warned that if he does this, they'll pit Rosberg first allowing for the undercut. So he bides his time, waiting until the final pit stops are completed. He then implements his plan. -- Now to us, we think that the Championship is still up for grabs and Mercedes have always said they will let them race ---- As Hamilton acts upon his plan, it becomes obvious to those on the pit wall that, this deal could fall though during the final race. They will not have their German champion. To throw Hamilton off slightly they point out the threat Vettel poses...he was quick and could possibly overtake for the lead...but I don't think he had the time, not for 1st. This makes Hamilton check himself, he speeds up for a couple of laps, only then to slow back down again once he realises that Vettel isn't threat to him, that he is only a threat to the Mercedes deal. This is when you get Paddy Lowe wade in with his 'instruction', which to me as the oblivious spectator, does not understand because the team have nothing really to loose. LET THEM RACE!
However, by this point it's too late, Vettel's tyres loose there grip and even Max starts to struggle. It ends Hamilton - Rosberg, and Mercedes have their German Champion in a German Car.
Now also note Hamilton's demeanour at the end of the race. He still was smiling, even congratulated Rosberg...none of which I would have expected! Was he smiling because he knew he was going?
That actually Rosberg was never truly a champ!
Who knows eh?!