I was early among those arguing that, after the Rolling Stone article, General Stanley McChrystal really had to go. This, I argued, was a matter of civilian-military relations, rather than necessarily to do with his conduct of the war.
Recently I spoke with a US-policy insider who argued that (notwithstanding the "war is bigger than any one person" principle) McChrystal's depature would turn out to be be a huge setback for the U.S. This was the case even though he had been replaced by America's most celebrated current military leader, David Petraeus. The elements of this argument, from least to most compelling:
1) Relationship with Karzai. According to this analysis, the president of Afghanistan likes and trusts McChrystal -- but is on bad terms with virtually every other prominent US civilian or military official. This sounds like Karzai's problem rather than ours, but: OK, point noted.
2) Rules of Engagement. Within the US military, the most controversial part of the McChrystal-blessed COIN (counter-insurgency) strategy is that U.S. troops should expose themselves to more risk, as part of minimizing "collateral damage" to civilians in Afghanistan. The point, obviously, is not to endanger the U.S. troops; it is to protect the local civilians in all ways. McChrystal, himself a famously fit and fearless Special Forces warrior, had the best chance of selling this policy to troops. Civilians and an "intellectual" commander like Petraeus would be less effective.