[spoiler=Other people's interpretation that I agree with]Madoka pretty much becomes a force of nature/a moe loli version of the grim reaper for magical girls and retcons history so that no magical girl ever turned into a witch by purifying and disappearing their soul gem before they become a witch and die. Becaue of that she retconned herself out of existence too so nobody really remembers her other than Homura. The new fixed timeline is overall better and magical girls don't suffer as much and actually get to fight for what they believe instead of pretty much just being cattle. In the ending scene, Homura is pretty much at the end of her life (notice corrupted wings), which is why she finally hears Madoka again, they're about to reunite.[/spoiler]
Also, I demand fanart of Cleopatra's, Queen Himiko's, Joanne d'Arc's, and Anne Franks magical girl forms >:O