Hm. Well. When I starting 5 skeletons, I am giving them names "Helium-He2", "Neon-Ne10", "Argon-Ar18", "Krypton-Kr36", "Xenon-Xe54" - of the noble gases. For Sadneil - "Uranium-U92", for Burn - "Plutonium-Pu94". For potential other skeletons - "Titanium-Ti22" and alike. I am bad with fantasy. But perhaps, somthing "usefull", with such a way, can be imprinted in the mind.
The one time I started an all skeleton playthrough (never finished) it was with the Freedom Seekers start and I sent them up to the Cannibal Plains. I just named them all after characters from Terminator (Kyle, John, Sarah and Reese), with the exception of one named "Arnold" and the Old Soldier character honest-to-God dubbed "Terminator". Since the goal was to exterminate all humans inhabiting the Cannibal Plains, I promptly named the faction "Skynet".