For starters:
Your saying that the purpose of Civ is not to provide an accurate view of history, but rather to entertain. But I fail to see why these two concepts are mutually exclusive. Can something not be both factual and entertaining? I fail to see why this game will be somehow more entertaining because of an illogical leader choice. I would be much more "entertained" by this game if the leader of the Byzantine Empire was an actual
leader of the Byzantine Empire.
Another point: "The purpose of civ is to appeal to the widest audience possible". What audience is reached by choosing Theodora? Women? They're already well represented in this game. In fact, they're represented disproportionately already. The woman:man ratio in this game is already far higher than in real life. I have no problem with that, so long as they're choosing female leaders that make sense. Catherine, Elizabeth, and Dido all make sense (and I don't know enough about Wu Zetian to comment). However, choosing Theodora just because she's a woman is hardly going to appeal to a wider audience.
Also, I want to eliminate your misconception that Civ is "no meant to accurately portray history". Yes, it's not meant to follow history precisely, but history is meant to provide context for the game. See:
http://www.playthepast.org/?p=593
And I'm not a salesman, but will historical innaccurracy really sell more copies just because it portrays a female "leader" that most people haven't heard of, and those that have know wasn't a leader?
I think the rest of my post already covered these things, but ok:
You would certainly be more entertained by more historically accurate or relevant gameplay. So would I. We are a tiny, microscopic minority. As I said before: Most people in the US get their historical perspective from things like TV shows and movies. Can you reconcile popular history with actual history? Entertainment with reality? Very, very, rarely. People don't go to theatres to see an accurate portrayal of the Battle at Thermopylae, they go to see a ridiculous over-the-top drama (a very entertaining one, mind you!) Most people aren't going to stop and say "But, that's illogical! It didn't happen that way!". You might! Which is good, I am glad for you. But most people are completely ignorant when it comes to, for instance, the leadership qualities of Eastern Roman Emperors and Empresses. These sorts of people are not excited by the prospect of learning about actual historical events or personas. They are interested in, for instance, watching brief, biased (and entertaining) documentaries and then trying to come off like an expert on the subject the next day at the office.
I'm not saying that you can't reconcile Entertainment and History. There are definitely forms of popular media that show relative respect towards historical consistency. They don't make much money. They target a very small niche audience, and they do it well on a modest budget. Civ is not that. Civ is a big, Hollywood epic in the world of PC gaming, and it cannot afford to pander exclusively to a niche audience.
Theodora being female has very, very little to do with choosing her as a leader; like you said, there are other, more interesting ladies around. Her being a figure surrounded by drama and intrigue, known for efforts to advance womens' rights in an era long before feminism, and for being one of very few Byzantine personas that Americans are likely to know about are the factors that make her the leader of choice for Civ 5 (also, she was in Civ 3; having a precedent is another important priority for leaders in the civ series). Are these "fair" reasons for inclusion? No. They are marketable. Is Theodora more marketable than a more competent leader would be? Yes.
That article, if anything, reinforces what I said. Historical accuracy is an extremely low priority for the civ series; it is a historically themed series, in much the same way that the Alternate History genre is historically themed. Civ takes loosely historical concepts, like cities and governments, and then goes on ridiculous tangents, like "Build museums and the Sydney Opera House to gain culture for the Utopia Project" or "Send your Pikemen, Horse Archers, and Riflemen on a 20 year trip across the ocean so you can conquer Gandhi the immortal warmonger before he builds nukes". If you consider these as harmless abstractions but have a serious problem with a less-than-ideal representative being chosen as the leader of a civ (which is itself a tradition dating back to civ 1), then I am not entirely sure what to tell you.
Xen said:
Because she lived before Emperor Heraclius, shes not actually Byzantine. The Byzantines did have a few female rulers to choose from (Like Zoe), but Theodora is like making the wife of King George the leader of America. Shes the ruler of the predecessor state to Byzantium, the Eastern Roman Empire.
Most Americans would not know the difference between Byzantium and the Eastern Roman Empire. Most Americans do know the difference between England and their own country (if only at a very basic level). So, no, it isn't like that. It's more like, say, having "The Golden Horde" as a civ and making Genghis Khan the leader. Most Americans wouldn't notice: "He was that Mongol guy, right? Cool."