Would be interesting and pretty unique! I'll add it to the list.
Now onto the bad news
I did some playing around with the custom cities, and found that upgrading another city overrides the faction creator you set in the strat map, so Thessalonica turned into Constantinople when I upgraded it to huge. Silly me as I was focusing on testing the upgrading for the unique cities.
I've been digging around for a solution or alternative way to get the cities in, but it appears the engine is just limited in that respect. The only options are:
1) Not have any unique cities
2) Sacrifice a faction for each unique city
3) Reserve huge cities for unique cities/capitals and they start out with huge walls, none of the prerequisites to get them would be needed, so they don't start out overly powerful than they should but obviously at an decent advantage. If you start a capital not as huge, once it gets upgraded it becomes unique (the problem is if you capture an enemy capital and upgrade, it will get your unique capital e.g. Venetians capture London and upgrade it to huge, London will look like Venice.
Looking through the files in mods with unique cities, I believe they've just gotten around this by limiting upgrading entirely and/or using unused factions, which I think takes away from a lot of aspects of the game. For SSHIP all the factions are used. Rather than limiting huge walls to only unique cities, you could always have lower level walls provide the next tiers perks so non-unique capitals can upgrade to an equivalent huge city e.g. large walls provides huge level defences and buildings, a village provides town level defences, buildings etc.
I kind of like the idea of capitals being strategic plus the bonus of them all having unique city models, but depends on what the Devs for SSHIP are comfortable with in order to get these cities onto the map.