Way too many hostile encounters with powerful weapons, like raiders with assault rifes, ghoul crazies, mercenaries, marauders and press gangs roam the wastes. Also running in brotherhood patrol while they are hostile is pretty much insta death to any evil player. I don't know what their role is other than cause random deaths to poor players. It encourages players to play in turn based mode just to get away from them. It's time consuming because then you have to run away from harmless encounters in turn based aswell.
Can't really think of any reason why there has to be so many deadly encounters other than please some extremists. The question remains what to do with them.
Make them rarer? Wasteland is HUGE place and good equipment is scarce. It shouldn't be that common to run in group of well armed people so often.
Make their territory easier to avoid? You should be easier notified that certain area belongs to this and that faction, thus allowing players to avoid them. I mean Blood gang members don't just come to joyride in Crips territory unless they really want troubble.
Make players always able to run from them? Spawn player closer to exit grid.
Leave it? As mentioned.
Do something? Nothing above, but something has to be done.