I list my personal preferences for unit changes at
Main objectives - overview - Provide a more consistent challenge throughout the game (rather than the early game difficulty spike and routine late game victory often offered by the default settings). - Make random maps more viable by reducing having to abandon a game as being...
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- Scout – given defence of 1 (to increase power of Expansionist Trait)
- Jaguar Warrior - enslaves (for flavour, add feasibility as a unit in mid-Ancient Era)
- Legionary - +1HP (legendary military unit for a truly legendary Civilisation)
- Keshik – increase attack from 4 to 5 (legendary military unit for a truly legendary Civilisation)
- Explorer – available at Map Making (to increase appearance rate before maps are shared)
- Galley / Caravel / Galleon / Carrack / Transport– carry capacity increased (to increase threat posed by AI attacks on other islands / continents and reduce player admin)
- Infantry – defence reduced from 10 to 9 (to increase attack viability of cavalry and marines to prevent a period of extended defensive dominance)
- Paratrooper – attack increased to 6 from 4 (to try and increase usage)
- Modern Paratrooper – attack increased to 8 from 6 (to try and increase usage)
- Bomber rate of fire reduced from 3 to 2 and removed lethal land bombard (to reduce power)
- Flak air defence increased from 2 to 3 (to counter Bomber strength)
Some the above changes are connected to other changes though. Primarily the difficulty setting changes (AI more productive but start with less units, makes change to scout more relevant) and tech changes (to make Swordsmen appear later and make early game combat with archers, chariots and horsemen).
Whatever your preferences I cannot recommend spending time with basic settings highly enough. It's pretty straightforward and can give so much more variety to the game.