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Ooh, age of empires - I've heard a lot about the franchise but haven't played any yet, will have to add them to my ever-expanding list of games I need to play :p

I can definitely see how the concept would somewhat force you in an RTS direction, and I commend you for seeing the idea through regardless. I generally have a bit of an opposite approach in that I always try to iron out a gameplay concept first, and then layer appropriate visuals/story on top afterwards (Unforeseen consequence of having Aphantasia, I guess).

As far as balancing goes, don't worry too much about the numbers - that stuff is primarily for multiplayer games. Just make sure to keep it organized in such a way that you can make a backend for adjusting difficulty in the future. A super easy way to fine-tune the difficulty is to add a Postal 2 amount of difficulties (search "Postal 2 difficulties" if you're unfamiliar) and have people decide on a sweetspot for themselves. 

The one aspect of balance that I would be mindful about is randomization. Don't randomize features unnecessarily, as being rewarded for spamming "Restart level" isn't a particularly engaging feature (I'm looking at you, roaming enemies and pillories/stocks).

Aside from that, here are a couple of suggestions for you, as far as the current state of the game goes, in no particular order:

1) Try researching/messing around with Foreswing vs Backswing, as well as Hitscan vs Projectiles - Understanding more about these mechanics and their implementation helps a ton. 

Playing some Battle Cats can give you a good understanding of the importance of Foreswing vs Backswing, and Starcraft 2 helped me learn some of the niche differences between projectile types and hitscan. 

2) Try refining the Sex mechanic to feel more intentional/deliberate - maybe through tying it to either control groups or unit actions? An easy implementation might be to have a hotkey with 3 cases: (1, 2, and >2 units selected)

3) Having waves continue after you finish an altar seems unnecessarily stressful, especially for lower difficulties. Maybe consider an approach closer to the Sky Shield mission in Starcraft, where reinforcements are sent to each encampment after an altar is cleared. 

4) Include a "Sniffling" CG for some story characters, to bridge the gap from uncontrollably sobbing to cheekily smirking

This one is more of a suggestion than advice, but:

5) Some roguelite/metaprogression might be nice, too. For instance, maybe a set of perks that could give m/m, m/f, and f/f relations different bonuses

Maybe a perk with a downside of monogamous sexual relations might be interesting too

Feel free to take whatever you want from this autistic rambling of mine, and I hope I managed to inspire - even if it's the teeniest little bit!