Check out the Clarus Victoria games, especially Predynastic Egypt. It's not quite a city builder, but closer to Civ. You start from building a settlement - some basic fields, huts, cemeteries, temples, barracks, and so on. It's nice, the map changes based on progress, and you end up growing from a city to taking territories up and down the nile.

Marble Age is notable too and has some mechanics unique to the game. Story is mostly the same, but there's three city states with slightly different tech trees. E.g. you'd need to fight the Persians at some point. Athens would be the classic path of farming, making alliances, building a wall and armies. Spartans need to raid for slaves for growth, but hold off on killing neighbors before facing Persians. Corinth would be more trade based and consider buying mercenaries and buying out the other city states.

I've bought all of them because they're an excellent ratio of time for fun as far as games go.