Against priest siege as Atlantean, I recommend advancing quickly (6 or 7 citizen up for 3:55 / 4:30) and producing a small army (~6 units) straight away to stop your opponent from hunting outside his base. If his starting gold mine is exposed it is great if you can put a lot of pressure on that as well.
After that you want to grab your 2nd town center and go up to heroic quickly (as opposed to grabbing a full population army) so you can produce Contarius and Arcus. When you see the Priest Siege coming, get watch towers upgrade and wall chip your towers and get pierce armor upgrade at the armory, and also raid his gold mines when his priests move out.
Make sure you use all your valors and try not to lose your heroes so they will be around to help fight off ancestors and eclipse. When Siege towers get near your town center, use Citizens to pick them off, but be careful not to let them chase too far after retreating siege towers. Also make sure any Pierce damage units you have (arcus, turma) are not targetting siege towers since they do negligible damage to them.
This strategy is tough to defend as Atlantis, but there are many strong Oranos players who have taken games off strong Isis players, so no, this isn't an auto-lose situation for atlanteans like you describe. You will need to macro, micro and scout well to beat a well executed priest siege though and always be on your toes about what's going on.
Villager rush on extended edition is not very effective because Atlantean TCs have more hitpoints. If expecting a villager rush, keep your Oracles at home so you can Valor them if he does a villager rush and immediately have some units to defend. Micro your town center onto his pharaoh then his villagers and try to pick off the wadjet with your oracle heroes.
Repair your town center with a citizen and build army in the meantime.
Don't resign if he takes your town center down, he will lose a lot of villagers in the process of doing so and you can constantly harass the villagers with turma that are now in your base even if he gets a town center up so that it's extremely hard for him to gather anything with them, rendering them useless.
Kronos rush depends on what God you are playing, you need to be more specific, but general advice would be to put your temple somewhere obscure and hard to find so he can't deconstruct it. You can read the score to see when he advances; since when advancing his score will dip (This can also mean taking a 2nd town center, but doing so will cause his score to dip more than advancing so you can tell). If he is advancing earlier than 3:30, it is likely you will face a lot of early aggression so wall off your gold mine.
As Greek - you want to get your heroes out asap to defend, the ranged one is especially important as it can zone out prometheans from your base completely.
As Egypt - Defend with Pharaoh, free watch towers help a lot so build houses around them to protect them. Build barracks and axemen/slingers or extra priests if you have to.
As Norse - Probably has the toughest time defending the Kronos rush. Make hersirs while advancing to defend against the intial oracle/prometheans and try to advance quickly. If he gets a good deconstruct on your temple it is really bad for you since that will be your source of early military. Don't be afraid to make ulfs out of your Town center if necessary.
As Atlantean - keep oracles at home so you can valor them if he rushes, aim for a 3:55 or 4:30 advance time. If you know you are being rushed try to build your buildings closer to your town center so they are protected by it, or put them to protect your starting gold if that is vulnerable.
note that on a lot of high hunt maps you can do a 6 citizen 3:55 advance as Oranos with Hunting dogs still by using up all the hunt in your base and not gathering any more than the bare minimum amount of gold/wood than you need to, which is worth doing sometimes to defend aggression or to be aggressive yourself.
Hi[This message has been edited by Sword of Scarlet (edited 10-09-2019 @ 02:49 AM).]