Magic may no longer base sets directly off real-world history (that ended a long time ago with Arabian Nights), but with top-down blocks, adaptations of real settings with a Magic spin is an oft-used ploy. No one would argue that Theros is really meant to represent ancient Greece, of course, but it's obviously a primary influence. Then again, such sets have tended to visit well-trodden and familiar places (the aforementioned "Greece," "Japan," "Transylvania") that are often used as the basis for fantasy stories. But the number of historical time periods and places to choose from is staggering, since history has been, well, a long time. Here are a few more original ideas.
The American Revolution. Sure, some Magic sets have covered the broader rebellion-against-government plot (hi, Mercadian Masques), but in a sort of morally rigid way; in that case the Kyren Goblin rulers and their Magistrate were obviously bad and the Cho-Arrim Rebels were obviously good. The American Revolution was much more... complex, and full of iconic moments (the Boston Massacre, the Boston Tea Party, and a lot that didn't actually take place in Boston as well) as well as memorable individuals on both sides that we know the personalities of in America by the time we're in about the fourth grade. A plane divided between a colonized, stirring rabble on one far side from an increasingly unstable but well-intentioned government on the other by a vast sea, with Magic versions of Ben Franklin, George Washington, and King George III - the result could be something like a morally ambiguous Scars of Mirrodin block, with convincing arguments on both sides and shifting ties pointing towards an uncertain future.
Qin Dynasty China. Qin Shi Huang Di, the first emperor of a unified China, was a real historical Byronic hero - he unified the "warring states" and brought order to a country that was until his rise wracked with the feuds of petty warlords, but then turned out to be an utter tyrant who burned books he disagreed with as well as burying their authors. Everyone knows that he ordered the construction of the Great Wall of China, in which thousands of workers died, and only slightly less well-known is the story of his quixotic hunt for a potion of immortality at the end of his reign. This period would be a great place to focus on the personal torments of the antihero who becomes a ruler, as well as some court-intrigue subplots involving the powerful bureaucracy.
The Space Race. This might be way too sci-fi for Magic, but hey, they figured out how to do two worlds (Mirrodin and Esper) where everyone's a cyborg in-genre. Instead of outer space to explore in this instance, we have the Blind Eternities, and everyone wants to see a Magic-ized version of Soviet Russia. Upgrading artifacts in a technological arms race sounds like a fun mechanical theme, and interplanar ships - maybe even warships - are an awesome plot culmination.
The Biblical Middle East. Yes, with all the begats and smitings and so forth. Making a fantasy version of this setting without offending the real Abrahamic religions would be a thin line to walk, but there are a lot of stories to possibly focus on, like the Exodus and the Ten Plagues of Egypt, the subsequent desert wandering, the building of Solomon's Temple, or even the rages of Samson. Anything in the New Testament, though, might be too controversial to even consider.