My main balance issues (mostly obvious ones that have been suggested many times)
a) Hippus horse mercenaries, way too strong. Fix with some combination of: no more metals bonus, drop strength by 1, double cost, limit generation to one per turn.
b) Insanity of elves with ancient forests. A partial solution is a *big* nerf in the time that it takes for forests to spawn into ancient forests. Forests mean that health is irrelevant and give big production bonuses, ancient forests provide crazy food and mean that you can cottage everything and have high food, gold and hammeres, and then the GoN civic makes happiness irrelevant too.
c) Many useless civics, partly because civics upkeep costs are so high that its almost never worth using anything with high upkeep. Positive health upgrades are also pretty useless considering their upgrades.
d) Weakness of archery line. Either give them bombardment, give them a free shock promotion or give them a couple of free first strikes. Or try something like attacks of opportunity from civ3, let them take a free shot at anything attacking their tile (so massed archers are very hard to break)
e) Weakness of drill promotion line. Add 5% strength bonus at each level.
f) OPness of stack effect spells. Chalid is insane and is available way too early for his power, maelstrom and tsunami are also very OP.
g) war weariness seems broken. why do I get very high war weariness from capturing enemy cities, and from my summoned units dying (could be imagining this). don't know if 3.17 changes have many any difference here. As long as my soldiers are doing fine and not suffering casualties, I shouldn't be suffering war weariness. Think c19 British empire jingoism - no-one in London is unhappy as soldiers are off conquering Africa and India without losing significant soldiers.
Also, war weariness needs to wear off faster.
h) very very high costs for some high end techs, like the tech for phalanxes (after mithril working, dont even remember the name) or the tech for immortals, or similar. Also; marksmen need mithril?
i) some underpowered buildings. weaponsmith, for eg. Often insufficient reward for investing in infrastructure, and hammer costs for buildings are very high given how few boosters for hammers there are (and how unavailable engineers are - no equivalents to levee, railroaded mines, industrial park, factory with power, etc.).
I also think that the single biggest AI weaknesses comes from a) their inability to prioritize education to get some cottages up early -> very behind in tech.
b) Inability to abuse Agriculture civic by farming grasslands and cottaging plains c) overexpansion leading to high maintenance costs and armies of warriors paying upkeep d) willingness to throw huge stacks of units at well-defended cities with walls. AI should evaluate the cumulative probability of victory before such a frontal assault, and if there isn't a good chance of taking the city it should just pillage instead - I hardly ever see AI pillaging effectively, especially with horseman type units (move, pillage, move back to stack). AI needs to learn to bombard with catapults better, mostly it just throws them into the meatgrinder with little effect.
It seems like the AI makes a decision about sending a stack to a city and starts moving the stack towards the city, and then doens't re-evaluate if the city is reinforced before the stack gets there in such a way that the assault would be futile.