Nothing makes it better or worse than anything else. A well done Encounters system based upon the old version is possible, so there's no reason to change from the original - which is generally what we try to stick to.
I think having a factor in the NPC generation so that the worse your Rep is with whoever it is, the more of them spawn and the harder Encounters get. The first main job is to edit all the protos so that you don't get so many NPCs who can't defend themselves, then it will be adding Perk capabilities so we can give some NPCs protection against crits (and stop them being crippled so easily, and then Farmed) and then tinker with the amount of NPCs who are generated in the encounter - specifically factoring in Rep and tightening up how it works for multiple people hunting.
After that it would be great to add someone else's idea (I've forgotten who it was, sorry) and have mini quests quick off from inside encounters at random (also increase the dungeon aspect too).
Any system where we can make them more random will just increase the re-playability of them, which is very important when you are going to be getting so many of these encounters over your virtual life.