I've read about insurgents use of motorcycles before. How much of a mobility advantage does that give them and what can we do to counter it? (I know this question is off topic but since you guys are both here I figured I'd ask.)
Everyone in Afghanistan would have a weapon. It is macho. Therefore, if they were on MCs, they would pass off as any other villager!

Only way is to stop them and question them. But that would mean many average chap will be harassed and it would not be good for the PR that is so essential for a COIN campaign.