I actually love that setting, I would definitely read something set in that world.
Let's start with a positive!
I love the unique nature of the setting you have devised, it is not often you see a believable time-frame mixed with high fantasy elements in the way you have done here. It makes a historical-fantasy that is somehow beyond historical. You have brought in some historical characters that will, no doubt, in some way connect us to the story more so than it would have done without such individuals. It's fairly cleverly done because reimagined historical figures that you describe are part of most people's cultural heritage in some way or another - I am English so I grew up with the background story of Arthur / Merlin, so the inclusion of Aurelius is already drawing me in. I'm sure the same would apply to others.
I suppose as a genre, Historical fantasy really plays on our expectations more so than the regular fantasy does, assuming that vanilla fantasy is an exploration of spiritual, emotional and ethical/moral paths and decisions that our unlikely hero takes. The bonus of this genre (and this setting) is that you are using civilisations that we think we know, and that we assume to know the outcome of, and you turn it upside down. I like it.
Follow up with a question!
How exactly does the high-fantasy element work with this? It sounds to me like a more mundane or dark fantasy rather than high. Maybe that is just to do with your synopsis so far, but magical elements do not seem to play a huge role in what you have provided us with, nor do any fantastic races such as elves or dwarves. I would reconsider looking at the exact sub-genre of fantasy this setting actually takes place in, and studying the common tropes for it's usage. You may find some things that may be mre beneficial to the telling of your story than just labelling it as 'high fantasy' because you think the type of setting demands magical action.
Remember! Only use something because your story needs it! Not because you think the genre does!
And finally, some critique
Now, this is going to be subjective, so you'll have to forgive me.
I always get a little bit of an itch when I hear the line: "The dark King/Queen/Emperor/Warlord has taken over Here/there/everywhere." It just seems too flat, too lacking in real characterised depth. I think this can link back to what I said before about the demands of a genre. Remember, you don't need to make this Dark Queen a Sauron clone who is utterly evil because you think that your story will not be seen as fantasy afterwards! Make sure if she is evil, she is evil for a god damn good reason, and not just 'because'.
I think your readers will be more involved and emotionally conflicted if there was not such a blatant evil vs good struggle (especially seeing as history, generally, is never a morally black-white tale), and you should rather inject a good deal of moral ambiguity into this 'Dark Queen'. Give her real, human, understandable motives beyond mindless psychopathy or lust for power. Why do real people do things that would be perceived as evil by their peers?. If possible, do the same for Alexander the Great! Don't make him the standard hero who fights for "Justice because the weak cannot defend themselves blah-dy-blah-dy-blah.". Chances are we have all read something along those lines as before, and I know that as a a reader, I want to see something new and original. Maybe he has ulterior, darker motives for wanting this woman out of power? Maybe he wants to usurp her but hides this motive under a guise of just rebellion. Maybe the Queen could be the force of 'good' and Alex be the force of 'bad'. Make it something that extends far beyond face value and you could be onto something very cool indeed.