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- We could spawn "native raiders" i.e. always hostile native units on the barb team. Place small stacks of them to guard goodies.
Where would they spawn? When I explore the map (I mostly play gigantic Americas map) the map is filled with native tribes and their villages. "Barbarians"/Wild Animals are hostile to the natives, too - so would those native raiders start raiding the next natives?
- Raiders could also target lightly defended cities.
How would they know which city is lightly defended? If they approach to scout and attack only lightly defended ones, sure - but please no beelining to the one city without a garrison.
- Pirates could raid coastal land (Arrr!)
Can player ships do that too? If not, no.
- Impose a "soft" distance cap by preventing units from healing when too far from friendly territory / structures etc.
Not "too far" - simply when outside your own cultural borders.
- Introduce ammunition to make non-melee units loose effectiveness unless regularly supplied.
Only if the AI understands that and does not send out ineffective units for not understanding that it would need to supply them.
- Ships should not heal unless when stationed in a friendly city \ port.
Historically usually every ship had a carpenter and a small store of wood on board for repairs. Masts broke, cannonball splintered through the planks etc.
Small repairs - or a limited amount of repairs should still be possible outside ports.