I know this is a pretty hefty topic (134 pages!) but I'd like to toss my five cents worth in. I haven't read all 134 pages, so some of these may have already been suggested. Apologies and thanks in advance.
1) Child units
My idea is that child units spawn randomly, say, for every male and female. They wouldn't be able to work or fight or anything (other than for the Spartans) but would instead provide a morale boost to nearby units, kind of like the female citizen aura.
2) Morale meter
The morale meter influences the amount of damage etc a unit has, and seeing other units dying lowers the morale meter. When it reaches 0, the unit panicks and deserts, becoming a Gaia unit. Children and Women would provide morale bonuses, as well as high HP and decent pay.
3) Currency
Each unit pays a certain amount of civ specific currency every say ten minutes or so, and the amount of currency a civ has is determined by their resource intake. Each resource would have a value. Say the Romans have 7450 wood, they would then have a few thousand denarii. Trade tariffs could also play a part. Mercenaries would also be hired with civ currency, and desert if they aren't paid on time.
4) Revolts
If the economy is terrible and general morale is low, citizens will revolt against you (turning to Gaia). There will of course be a loyalist faction made up of those with higher morale, but for every revolt, the chance of another increases.
5) Food
Give food a purpose. Look at Glest for example. Each unit in Glest uses up a specific amount of food, and when food is low, they start dying. A famine would lead to low morale which would in turn lead to a revolt. Soldiers would use up more food than others.
6) City life
Make general city life more interesting. Maybe even random events (like in Total War: Rome or Europa Universalis) i.e a religious festival (increasing morale) or a military parade.
7) Farmer units
Argicultural specific units. 50% chance of a male or female farmer unit being spawned. They'd have a boost when farming but be horrible at everything else. Maybe even child farmers.
8) Slaves
This has probably been mentioned a ton of times before, but have the option of when a unit's morale is 0, they either become Gaia units or become slaves for the attacking civ. A Slaver unit could be added for this purpose. A new building like a slave market or something could be added too. And maybe even a slave sale event and slave revolts.
9) AI banter
When playing a game against the AI, it would say things depending on specific factors like whether or not it is winning. If winning, it'll generally trashmouth you but if losing, it'll beg for mercy and such.
10) Bandits
AI bandits that spawn from a small bandit camp. Bandit heroes could even be added to. Bandits would raid trading routes and smaller settlements, but are weak compared to citizen soldiers. Their strength would be numbers and maneuverability.
11) Named units.
Generate random names for units. Like for example, a Roman Hastati would spawn with the name "Gaius Lucius". Names of course would be civ specific, wouldn't like to see a Mauryan with a Roman name...
12) Mounted units follow the road...and an option to build one.
Worker units (like Auxiliaries for the Romans, for example) would be able to build roads connecting settlements. When mounted units are moving, there can be an option for them to only follow the road, giving them a speed boost. The Gauls and Romans would have stronger roads than others, however (I think it's the Gauls who had strong roads as well, or was it the Britons?)
13) Splinter fations and civil war.
This includes the option of assigning an AI commander to manage a settlement for you, so you don't have to worry about it. If you don't support an AI governor enough, or if their morale drops severely, they may splinter off and declare war on you. They could also join forces with an enemy.
14) More heroes.
Self explanatory.
15) More other/ things for Atlas.
In some maps, you can find campfires and other cool looking things, but sadly they aren't in the Atlas map editor (at least, I can't find them).
16) Day/night cycle
Might be a bit too much, but a day/night cycle would look good. Skirmishers could have a stealth bonus when the sun's down.
17) Unit stealth
Units could have stealth bonuses, i.e. Skirmishers hiding amongst threes, Swordsmen hiding in the tall grass etc. Armour would also play a part, heavy units have less chance of sneaking than ligher units.
18) A more specific alert.
The alert should only have non-combatants to flee. It annoys me sometimes. The alert should also rally your troops together (regrouping at the civ centre where you sounded the alert) before attacking the invaders.
19) Enemy city gates.
Could the enemy lock their gates? It's more an asthetic thing for me.
20) Enemies siege walled settlements
If you have a walled settlement, the AI plans accordingly and lays siege.
-TheGreatCaesar