Welp, I've been playing my scenario from start to finish, at least once. I am doing this because I believe I am nearing Beta phase of the scenario. Which means soon you'll be able to test it!
I'm having tons of fun right now. Played Macedon, rushed Triremes, Archers, and Axeman and blitzed Athens and Sparta by turn 120 (they're not very easy to destroy + I've made some scenario changes). Macedon's trait really helps in warring the CSs, as your archers and catapults can really pound even Strength 17 cities.
Few issues with the scenario I've noticed so far, and I can't seem to fix them. And random thoughts:
1) On the select screen, you can only play as Macedon, Achaemenid, Hittites, Egypt, and Babylon. There is no option to play as Phoenicia or Random, and I really need that bug fixed, since Phoenicia is my favorite civ. They're playable just fine on a random game, but not the scenario. Playable box is checked. I don't know what the issue was, it stopped working like last week.
2) I've removed the whole starting techs/units thing. It was unbalancing the early game and I wasn't happy with it. So I kept the +6 Happy from Palace, started you off with one warrior/settler and I'll let you expand at your free will. It also keeps beelining the tech tree from happening (for a point of reference, by turn 60 I was working on the 5th column of the tech tree, and now on turn 120 I'm just finishing the 4th). I did this by increasing Classical and Late Classical Era costs by a ton (the jump from Ancient to Classical is 60 beakers to 275 beakers). And as it's looking, Late Classical has to jump from currently around 700-1700 to the neighborhood of 1200 - 2500. I'm still tweaking the figures but the scenario is flowing much more smoothly than before. I've had a blast so far warmongering on my city-state neighbors.

3) AI civs need to be warring more. Ancient times were much more violent than what they are now. I'll be upping expansion and war flavors by a bit to make them more likely to attack each other. As it stands, Mitanni is a war freak; he declares on everyone yet fails to make a push. Which is good; Mitanni in history only lasted for a hundred years before getting rolled over by the Hittites, I think. He's also smack dead in the middle of three empires, so it creates a lot of tension. Very happy I added them.
4) I'm very unsure about policies. At the moment they seem overpowered, but I want to keep them this way because of how short the scenario is. In fact, I've been thinking about upping it to 500 turns! But I'll have to wait and see, I have 280 turns left to conquer the Mesopotamian landscape. If I need to, I can make this scenario really long and start upping tech costs to compensate. I've been hesistant to touch production costs - in fact, I want to see lots of units, so unit maintenance may go down.
5) I've been doing some thinking, and I believe I want Mitanni, Lydia, and the Medes (NYI) to be playable civs. Mitanni will most likely be the hardest civ to play; their starting area sucks, their unique units are only cheaper, and their UA is modest (33% less land unit maintenance). You'll be able to spam a bunch of units, but Babylonian Bowmen, Hittite Three Man Chariots may tear them to pieces. Lydia plays similar to Phoenicia, but they get their gold from their improvements/buildings instead through trading (Phoenicia focuses on trade route gold, and Great Merchant gold).
And because college is coming around the corner, I want to put the mod in your guys hands to give me feedback on it so I don't have to work everyday to balance it.

I can't wait to push this out to Beta, it's almost there! I need to finish the Trade policy branch, then add the Medes, and then fix this scenario issue.
My apologies for the wall of text.