My suggestion is to add rare bosses into dungeons like sierra, ares, warehouse, glow.
I mean those npcs would have better RANDOM resists, so one day it will be almost immune to flamer or energy, another day to normal etc.
Respawn would be very rare like special encounters are now.
Killing that boss would provide getting achievement, something like +1 extra healing rate, +1 hp, +3 flat dmg vs deathclaws, enclave patrols<-- just something symbolic, not breaking balance in pvp. Bonus would be given only once.
Those npcs would have large variety of loot like weapons, drugs, armors maybe ammo or caps, not t4. Simple harder bosses (enclave general or BoS paladin or even Frank Hooligan) would give better loot, easier(ghoul Harold, Kaga ) worse loot.
Boss would stay in location for maximum hmm 30 minutes?
Lets talk about that idea.