EDIT:POSSIBLE SPOILERS...
Yeah I agree, more hostile human groups ! And the rare encounter with wondering super mutants on their way to Black mountain.
I'd love to see the random raider groups that you encounter around Prim/Nipton/Novac become a more prevalent threat around that area, as you gain levels there continue to be random ambushes but with larger, better armed groups as you level up.
Random hostile, heavily armed and well equipped mercenary/prospector groups would be great to see occasionally too, to keep you on your toes. I'd love to see these groups randomly ambush your character if your carrying a large loot haul or just made a lot of caps. Maybe even follow you a while as neutral to hint of a possible ambush and for the speech savvy you could confront them and use the under utilised terrifying presence perk to avoid a confrontation.
I reckon the fiend territory could use much more random encounters of fiends rather than the very predictable locations and maybe after the fiends diminish there could be a bunch of prospectors that appear in the area with the occasional prospector turned junkie groups that may or may not become randomly hostile towards you in that area.
And what happened to the ranger/legion assassins ? It seems like the first time I pissed off the legion just one group of assassins jumped me then I never saw them again. As for the rangers, they threatened me with three days to clean up my act and three days became a week and before anything even happened I was given a pardon by all the major factions... These guys should bring the worst of the best your way, attacking you any time and with the best equipped people in the waste once your at higher lvls. Rangers in full combat gear and sniper rifles

As for super mutants I think on the very rare occasion it would be cool to run into the odd, very defensive super mutant group. They wouldn't come after you but would fire at you on until you engage or leave them alone. Night kin could also make the odd random encounter, ambushing you at night around the Black mountain/Novac/188 areas. Travelling those empty dry lakes at night might become that much more interesting when Night Kin start hit and run attacks on you.