But Paragon/Renegade isn't a morality system, it's a reputation system that represents how Shepard approaches solving issues. Because of the larger goal being the same, Hence you can quite easily build a character within the system who cares a lot, but will always take the drastic approach, or a jerk, who will always choose the rigth appraoch. Thus I don't have similar issues with P/R system than I had with Light/Dark side in KOTOR, as that is a morality system and a very limiting one at that. I also feel that it is justified to have that behaviour be a limiting factor for future huge choices, as if your Shepard is a cold-blooded killer who just puts everyone down, having them suddenly be able to make others understand the value of mercy via passionate speech would seem quite of weird. What I would not want them do is to follow the ME2 system, where instead of looking at the absolute values they looked at the difference, which was a really weird approach.
I'm also not quite certain why the companion reactions are brought up here, as that is a separate issue from a morality system. What I would like, personally, to see is the ME team stick with P/E, but continue to build it and perhaps go deeper in to the concept of what do they want it represent, as I think that was something that got a little bit unclear in the shuffle. I also would prefer if it was mostly dictated by big decisions, not by reaction choices, and thus act as a definition of how the character approaches problems instead of how they act.