in Fallout 3 it may have been overpowered but there were only, what, 90 something mini-nukes in the Wasteland?
it would be good if they made that same low amount of them in the Wasteland and made the Fat Man just as overpowered as it was
but yeah, the skeleton idea would be cool as actual enemies. like there could be some sort of DLC to go to a castle or something like that?
another cool thing would be if at a big bank or two, big factions could hold a stronghold in there, so once you defeat them in that bank, you steal all their currency and weapons and ammo.