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I just had an idea which I don't know is good or terrible, but before reading this, the idea is for minor perks rather than anything else - not to give people a reason to join one city over the other, but to just translate flavor in game mechanics. I'm a huge fan of game mechanics and flavor being connected. Ideally, these would be no better than a minor trait, perhaps a bit weaker. I think it would be acceptable to have disadvantages attached to balance them a bit, although I haven't included any in this post.
Basically, the idea is that after being a citizen of a city for so long, you could get a minor perk related to that city. I could see a point in non-citizens having some perk as well, if something could be dreamt up for them. Perhaps after five years of non-citizenship, you would lose your old perk, and after five years of citizenship, you would gain a new one (meaning if you change cities every four years, you would never have such a perk).
For Cyrene, the advantage would probably be extremely minor cold resistance, or, if weather ever becomes relevant, perhaps improved resilience to cold weather. I'm iffy about any city gaining a combat advantage, but I think it would be ironic to give it to Cyrene, since they're likely to get the least use out of it. Being able to see better in blizzards could also be something, but it'd have to be minor, rather than outright making those artefact glasses redundant.
For Mhaldor, I think some sort of reduction in EXP loss from death would be cool, given how death, murder, and suffering have a strong place in their culture. I think EXP loss in cities has been turned on, so maybe they could have an exception to that - when a Mhaldorian kills another Mhaldorian, there could be no EXP loss or gain, or something, letting them be as gruesome to one another as they want without OOC concern. Of course, that might also reduce the impact of such executions.
I can't currently dream anything up for other cities. Ashtan and Hashan are exceptionally difficult, given their open-ended nature. Perhaps someone who knows more about Achaean lore can think up some geographical advantages related to where they live.
Eleusis could have some minor advantage related to concoctions, but that seems a bit obvious and combat advantage-y. Perhaps they could just have the ability to swing up into trees before learning the appropriate ability, and be a touch faster at it once they do?