My thoughts:
1. +0.5 f/sec gathering rate for each farm upgrade researched.
1. Add wooden shield in tool but remove iron shield in iron. Move impies to tool as an upgrade to bowmen and change their cost to match. This should weaken some tool rushes (sling rush, scout rush, tower rush), strengthen infantry vs bronze archers without affecting iron. The cheaper impies might also help some civs (carth, choson, roman) cope with bronze age better.
2. Add +2 shielding to the cav/hcav/cataphract line, which should turn them into effective archery counters in bronze and iron.
3. Increase the minimum range of ballistas/helos to 6, STs/cats/hcats to 8. Have engineering increase not only maximum range by 2, but minimum range as well. Reduce the damage area of the cat line, such that STs hit a single tile, and cats/hcats hit a 3x3 area. This should render catapults virtually useless as field artillery, and helos would require support from other units to do their thing.
4. Reduce scythes' base attack/armor/range to 7/0/0, like spear chariots. This should let them continue to raid priests and villies, but weaken them greatly against standard units.
5. Reduce HA and HHA damage to 4/5, and their gold cost to 50g. This should bring them in line with other archery units somewhat, and they still have +2 shielding.
6. Remove the ultimate upgrades for both infantry types from normal play. They are neither realistic nor balanced.
7. Add iron pellets in bronze, 100f 200g to give slingers +1 attack and +2 range. This would allow slingers to keep up with archery upgrades.
8. Automatic short sword upgrade. This means swordsmen would be available the moment you hit bronze (before they can be easily countered), giving civs like choson and rome a rushing edge.
Civ changes:
1. Greek - All boats +30% speed, so they have half an economy. +2 slinger range to give them a good tool rush unit and bronze archery counter.
2. Choson - Change swordsman bonus to +50% swordsman hps, so they have a bronze unit worth mentioning. Change tower bonus to +2 range and +2 attack, the latter being more useful in tool and bronze.
3. Carth - Replace transport bonus with -20% age advancement cost, so they can rush through the ages with a smaller economy.
4. Hittite - Add impies and slingers, remove camels and eles. Reduce warship bonus to +2 range.
5. Phoenie - Increase woodcutting bonus to +25%, remove slingers and cavs.
6. Shang - Add alchemy, ballistics (and ballista towers). Remove camels, nobility (and scythes).