After some update (probably wipe) all sorts of companions, mercenaries and other followers will not attack players - even if attacked directly. At the same time, some nerfs from the past will go away, so it will be easier to use followers for PvE purposes.
And if somebody wants PvP, then he should do that without help of NPCs. It should solve all problems with PvE in PvP, while not making it harsh (again) for PvE players.
Few corrections Mercenaries will be able to engage players, they are one-use anyway. However, as mercenaries are NPC, they could be countered with companions etc.
I really would hate to see companions be basically removed entirely from PvP, and mercenaries just aren't nearly as interesting as they are now to be used to me. It may be too late for any hope of this suggestion if Kilgore has already put a lot of work into a new companion system, or maybe this would be too much work, but would hurt to at least put it out there I figured. Mainly I'm hoping to maintain build variety, and preferably even increase it some.
I just figure put a hard limit of 1 "NPC companion slot" and provide a few more options of variety. Having a companion requires a minimum of 3 charisma so that it isn't just a free bonus for everyone, people have to specifically make the decision at character creation. Preferably companions will respawn back at tent, but would still drop everything they were carrying.
There would be some options of very weak companions, that come as a preset group. Like I can pickup a pack of 3 dogs that follow me around, and will fight players, but counts as the "1 companion." Being dogs they're ridiculously weak, and probably wouldn't be much for PvP but still provides a nuisance with their speed and numbers, like real dogs.
Certain companion types will be limited in weapon options. Such as you can get a squad of 2 tribals, but they can only use fists or spears, and can't wear armor. The individual companion options which you can only have 1 unit would allow more variety and options. Super mutants if allowed are just a hulking meat shield capable of certain weapons as their model permits, but cannot wear armor (think marcus from fallout 2). You can just pick up some average joe who you can deck out in any weapon/armor you might have as well
Charisma would provide bonuses to companions, perhaps something like a natural 3% DR per charisma, but mainly create a handful of perks that have charisma requirements that benefit companions, such as...
3 charisma requirement,
Animal Magnetism non-human companion's respawn time is reduced, and will join you on map generation rather than requiring a trip back to the tent
Spotter- Your companion's vision range is added to your own
Hidden weapon installment Any robot companion you have will occasionally use a hidden weapon you can install (shoot a single rocket, critical strike with cattleprod, flameblast as if from a flamethrower, depends on what item you give in the offhand. Can only very rarely use unexpectedly, but can be ordered to attempt to use the secret weapon when low on health, when master is low on health, when the target is low on health, or at the beginning of a fight.
Emergency repairs You can use the repair skill on a robot companion to heal some damage. Possibly require 1 metal parts and 1 electronic parts in inventory
Painting the target Your companions will attempt to strike the same target/body part that you last attacked
Unexpected strategies Many armor designers never considered someone would actually bring a knife to a gun fight...companion melee attacks has a chance to pierce 50% of the target's DR without requiring a critical
5 Charisma requirement
Like Rabbits Animal companions in groups of 2 or more gain an additional animal (so 2 dogs/geckos become 3)
Follow my lead Armorless companions will enter sneak when you enter sneak. (not sure how possible this is considering sneak currently requires the wearing of leather armor, but I'm thinking an ambush of dogs or tribals would be cool)
Watching their back Your companions bonus DR based on your charisma increased from 3% to 5%
Inspiring attack Your companion's attacks ignore 2% of the target's DR for each charisma point you have
8 charisma
Learning from the best Your companions gain all of the offensive perks that you have (bonus critical, critical rolls, bonus ranged damage, etc
Following in your footsteps Your companions gain all of the defensive perks that you have (toughness, adrenaline rush, man of steel, In your face, etc. Lifegiver might probably be too overpowered with the multiple companions though, although they would be really weak to begin with since their initial power/usefulness is meant to be divided by the 2 or 3 companions
Some of the perks are meant to be strong, such as the last 2. Having to invest 8 charisma is far more than anyone ever does now, not to mention that you would be short of the bonus perks players normally have since presumably they would be investing some into other companion perks, or at the very least short 1 or 2 to grab the 8 charisma perks
It requires some more work and balancing probably, I didn't really detail the variety of companions since the rumors of post wipe update as well as a few of the other suggestions that mentioned things like pigrat companions suggests a planned update some day with more follower types.
Its getting late, but if this is well received I'll put some more effort into it, cleaning up the presentation and coming up with more perk ideas.