Dido and Hannibal both have their problems (one is legendary, the other was a general not a political leader), so I'm fine wih Dido getting the edge there.
Hannibal was a political leader after the Second Punic War. It wasn't for a long time, but he ended up being a great reformer (his problem was he did too much too quickly and pissed off both rival political leaders and the Romans). On top of that, he ruled New Carthage as his own little fiefdom and the Barcids were influential political actors in the Carthaginian oligarchy for generations. He's a far better choice than Dido, who may or may not have existed (I make the same argument for Gilgamesh, fwiw). Hell, while I'm not a fan of Cleopatra, she is clearly a stronger choice than Dido. She's actually a stronger choice than Theodora too (I wouldn't go with Justinian either, I'd prefer an unequivocally medieval/Greek ruler rather than the guy known as "the last Roman Emperor.").
I was giving this some thought on how to make suggestions beyond the usual ones. Europe seems to come the easiest with Elizabeth, Isabella, and Catherine being just as good as any male choice. I also think Boudicca is a no-brainer if the Celts are included. But I wanted to think of some choices outside of Europe.
To me, it's likely we'll have one Southeast Asian Civ. In the past, Firaxis has gone with Khmer in Civ4 and Siam in Civ5. For Civ6, I would go with Vietnam with Trung Trac as the leader. Usually, the Trung sisters are portrayed together but, if one is considered the primary, it's Trac. I think she would be a fun change of pace (plus, she'd be riding an elephant, which is badass). I also think, if they bring back Indonesia, that there are some strong candidates for female leaders. ETA: Tribhuwana would probably be the most obvious example, but some of the Muslim Kingdoms had female rulers, iirc.
I personally would also pick Indira Gandhi if we're picking a Gandhi, but I know that's not happening and probably would be controversial anyway.
