They're so alike I wouldn't want to describe any of the four Caesar 3-games as "better". Different, certainly, and harder or easier.
Caesar 3: Often considered the most difficult, partly due to lacking certain things like roadblocks (though gatehouses fill much the same function) and less fine-grained control over storehouses.
Pharaoh+Cleopatra: Sometimes also considered the most difficult, due to things like entertainment venues requiring intersections, broken terrain that is bi- and tri-sected by the Nile, water access restricts where you can build housing blocks, monuments to build, more goods, etc.
Zeus+Poseidon: By far the easiest. Does away with labor walkers, meaning you can place industrial districts without concern for labor access, reduces the amount of goods, monuments easier to build. Planning things in detail before starting a mission is less useful, as the game is divided into Adventures and you keep returning to the same city mission after mission, with new goals, interspersed with colony founding missions.
Emperor: Rise of the Middle Kingdom: Haven't really played it, but in keeping with Zeus, it lacks labor walkers.
These four, and no others, are the Caesar 3-likes.
Two more city-building games were made by sort-of the same people from Impressions under the new company Tilted Mill:
Children of the Nile: New Egypt game, this time more realistic and simulationist - there's no walker management, every citizen in simulated and they go get all the services they need, rather than having them delivered to them. So from a push to a pull system. Haven't played much of it.
Caesar 4: Also mostly does away with walker management, felt something like a cross between Caesar 2 and 3, IIRC. Has 3 types of housing, the poor doing the dirty jobs, a middle class doing nicer jobs, and the patricians that do nothing all day. IIRC.
There's also Civcity: Rome, was playable, but nothing special, as far as I remember.
BTW:
Here's a pretty good and instructive LP of a guy playing a map of Caesar 3, Pharaoh, Zeus, and Emperor. So far he has finished the Caesar 3 map and the Pharaoh map, and is well on his way to finishing a Zeus adventure.
