Although Brawn has had a very successful career, it should be pointed out his only success as team principal came when the massive Honda budget of 2007/2008 enabled him to spend an almost unlimited pile of money to develop three different cars for the massive rules change in 2009. Ferrari and McLaren, the only teams with comparable resources/money at the time were investing all their effort in fighting the closely fought world championships while Honda cut their losses, didn't do any serious development of their 2007/2008 models and used their huge resources almost exclusively on the 2009 rule changes.
It was the most expensive F1 car in the history of the sport by some considerable margin.
Although the season campaign was handicapped by the Honda pull out at the end of 08, meaning the car had to be adapted to run a Mercedes engine and run on the lowest annual budget of a championship winning team, inflation adjusted, in the modern era of the sport the base platform was so far ahead of the rivals (except for the Red Bull) that win in 2009 was only made possible by the huge Honda resources developing the car rather than the genius of Brawn.
That's not to say that he didn't play a part, because he did have to operate on a shoe string budget, but there was virtually no development of the car made during the year (HRT, arguably, developed their car more in a season than Brawn did, and I think that Button is the first WDC in a long, long time to be driving the same car in the final race of the season as in the first. So while Brawn does deserve credit for managing the team during 2009, this was more to enable it to turn up to races and race rather than a typical F1 championship strategy.
This is not to say Brawn isn't a competent F1 team boss, it's just to say there's no real evidence for it. The only success he had as team principal came under unusual circumstances, he can't be blamed for the poor 2007 and 2008 performances, because he played no part in the 2007 car development and then made the decision to focus on 2009 (so I guess he can be blamed for a poor 2008, but that was part of his plan, which worked with a successful 09)
Since 2010, the performances of the team have gone backwards. Although Mercedes won in China this year, it's worth pointing out they could have won in China the previous seasons as well (2010 Rosberg lost the lead by running off the track, and in 2011 the team underfilled Rosberg's car with fuel when he had switched to the optimal strategy first, and McLaren then followed)
Their 2010 performance was stronger than their 2011 performance and in 2012 they finished one place lower. So he hasn't had a good track record operating under Mercedes. Now, they might be a reflection of him not working well in the new environment that Mercedes has created (being a much more corporate, numbers driven team than Ferrari) rather than a reflection of his actual abilities in his ideal environment but even if that is the case, Mercedes now own the team and that environment is not going to change. So even if he is an amazing team principal it doesn't matter, all the evidence suggests he isn't going to deliver that for Mercedes.
However, there is no real evidence that he does excel in the team principal role - the area his genius showed was as Technical Director and Strategist at Ferrari. Of course, it is unlikely he will step down to this position at Mercedes (it is very rare someone would make a downwards move in such a publicly visible position, particularly in a company they used to own) so if Mercedes do decide he is not cut out to be team principal, or he decides he does not want to continue in that role, the only real choice for him is to leave.
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