I liked the firendly fire accidents. Made it more "real" somehow. Sounds silly, I know, but it made me think where I went, to avoid getting into crossfire between teammates and enemies. If just my team mates would have shown the same consideration every now and then
As for the control over team memmbers, FO2 got it exactly right for my taste. Give them general orders, limited by their personality and let them do their own thing. It felt like you and a party, Not you being a 7 headed hydra wielding 3 guns, 2 knives, 1 flamethrower & a gauss rifle at the same time.
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Friendly fire, sometimes your NPCs took it personaly and attacked you if you shot them Ian was good at that. He could accidently shoot you, but no you could not return the favor.