Ensemble has truly added on a lot of good qualities to the Atlanteans, but has left one critical weak spot, the Classical Age.
If you get tired of the Atlanteans owning in the later ages, follow my advice.
If you're Greeks and you want to beat the Atlanteans, make ten villagers and gather enough food to get you to the Classical Age. Then focus on wood and gold. Make several Archery Ranges. Then mass out toxotes like crazy. The only true weakness of Atlanteans is archers at this point. Maybe reinforce your army with a couple of centaurs. You'll win, trust me you'll win
If you're Egyptians, do the same with sphinxes and axemen
If you're Norse, do the same with Throwing Axemen and Einherjars.