Theodora was very defamed by Procopius and the rest of the Byzantine aristocracy because she was from the lower cast of the society, hence they called her a prostitute, when she actually was a circus worker.
She almost made the whole of Christianity to convert to monophysitisme - if it wasn't for the intervention of the pope himself. Besides she had a great deal of influence over Justinian.
However, I agree that the Byzantine leader should not be her. She never actually were the powerful person in the throne. Irene was, and in her laws she signed as an EmperOR- basileu, in the masculine, and not basilissa, in the feminin. But she governed the Empire in a low point, it wouldn't be logical to put her.
And Justinian shouldn't be the leader because, as most historians says he was the last great ROMAN emperor. ROMAN not BYZANTINE. Only after Heraclius the caracteristics of a byzantine civilization would be stronger. Therefore, I guess the leader should be Heraclius, who saved the empire from destruction, or Basil II, who made the empire rise to a level of recognition and prestige unparelleled since Justinian.