For those missions where we have to escort a princess, an Admiral, a bumbling engineer, a damaged ship, a spy, or other needy NPC, how about they follow us instead of us following them? If we're going to protect them, we should be up front taking the heat. And if we stop, they stop.
For those missions where NPCs "accompany" us, please don't have them follow so close that they're breathing on our avatar's neck. "Seriously, WTF close-walker?! You trying to give me a flat tire?!" Have them stand way back out of the way, especially in combat. When you've got Admiral H'RasMent sniffing your neck-hairs and you drop to 'Aim' all you see is their azz. At least have them crouch to 'Aim', too, rather than stand there like a plasma grenade magnet. As dumb as my BOffs are at least they get it.
Also, in a couple of the 'Escort damaged ship' missions, how about just the opposite? When we're ready to leave, they should go first and we should follow. Y'know, to make sure they get out okay. Nothing says we care like leaving before the disabled ship does.