The main problem with the Encounters are that they are not very well balanced in risk vs reward. A lot of them you can solo many times with very little risk of losing, so it ends up being a farming session rather than any kind of true PvE.If it stops being quite so easy then it stops being farming.I don't think completely chaniging the system away from the original is the answer anyway.
If you want to make enemies, try to change something.
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.
Bad Reputation just goes up before you feel any kind of pain because of it. Also nobody is after you, you just keep getting the same encounters like everyone else, with the same NPCs you can kill easily.
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.
if critters inside an encounter are strong, they are non-hostile anyway (Enclave, BoS, SF caravan)
Yeh, because lots of people had problems with it. That's why it was adjusted to be like that in the first place. Guess players don't like it to be limited to some zones, but want to go to every place.