Assassins Creed does not make historically accurate games. They make fantasy games set during fictionalized historical periods.
Their depictions of every historical person has been wrong, since the first Assassins Creed game and up through this one. Guess what, none of the Popes depicted as the bad guys from Assassins Creed 2 series were sniveling, dastardly cowards sacrificing human meat for the pursuit of power (that isn't to say Rodrigo Borgia was a good guy, but just that their characters are heavily fictionalized and based on the popular presentation of them in media, not historical accuracy). They typically take the popular recreations that pop-media has given us over the last couple centuries of books, television, and movies. Borgia, in the Assasins Creed 2 series, is presented as a sprightly kniving, fresh faced evil-looking pope because that's how Borgia was represented in films from the 1950s-1970s. Most recently, BOrgia was played by Jeremy Irons, a much thinner, older, politically-machinated character, and I'm sure if Assassins Creed 2 were made after Irons' presentation, that Borgia would follow that characterization.
Cleopatra as the exotic Mediterranean beauty who woos Greek and Roman royalty is the pop-media characterization of Cleopatra, and Assassins Creed is carrying that tradition through. She's typically been played by Westerners in media, going back to the 30s and 40s, and so our popular recollection of her is different than how she probably was, and our tastes today are different than what a person's tastes would have been 2000 years ago. If this exotic beauty is presented as someone who is not exotically beautiful to contemporary players of the videogame, then you lose some of the motivation for the character.
Beyond that, Assassins Creed has the out that these are (generally) the shared memories of the characters in the story, going back through their shared, technologically reconstructed DNA. In past games, especially the Pirates games, they've reconstructed parts of towns and islands that didn't exist at the time that the story was set, but they cleverly (or cheaply) explain it away as "this is part of the collective re-imagination of this area." One that stuck out to me was from Black Flag where the knowledge database explains it away as "This monument wouldn't be built for another 30 years...... but it was just too cool to leave out of the simulation." If buildings, islands, and entire family lines can be made up so that they construct a better 'simulated memory,' then it stands to reason a character could represent our collective memory, and not necessarily be an accurate representation of what she may have actually looked like, dressed like, or acted like. At least, Assassins Creed has done that with all of their characters before.
