Methinks you sell them short. I like a good number of those ideas, at least as options. E.g, a small chance for bow FF on front-line melee, if they are aiming close to your own crew. Darkness is another one I've raised before too; I hope that makes an appearance (when situationally appropriate).
Friendly Fire can be a mess to balance, go play some of the original Fallouts where companions can be deadlier than any Supermutant or Deathclaw, then tell me how great a FF system can be. Getting killed because one of my companions decided to stand behind me and fire on full auto because I was being flanked by three Supermutants and he wanted to hit all three at once is spectacularly annoying. (I will be polite and just say #%$@ Ian right in the $@#*%%$@ .)
Getting killed by a super mutant shooting me in the face with a rocket launcher, or because a Deathclaw ripping my face off is something I can live with. I can level up, get better equipment, and just get good at the game. Getting killed because of lousy companion AI is just frustrating, because I can't really defend against that. Short of giving companions crappy weapons, which kind of defeats the purpose of companions
With a decent AI system, that considers things like party positioning before cutting loose, then a FF system might be a somewhat decent idea.
OK, so as for what I would like to see in PoE 2, I would like to see more party wide skill checks. Yeah, my main character may be lacking a bit in X, but it seems like in some situations their companions could step up and explain things.