I believe that different weapons with different names (and, if possible, different values) would already be enough, as maybe different guilds.
Let's take, say, the vikings. For their quirks, they could have superior bows, better weaponsmiths, great tanning, but inferior metal armor. The japanese would be different, maybe capable of producing katanas, and so the "europeans", with crossbows, gothic plate and stuff.
I believe the trading faction concept should stay, as there is no reason for it to go away. Maybe the different human factions always keep a trading, maybe as a form of a multi-national quasi-company run by the guilds? That way, you wouldn't need to change neither the guilds or stalls, but would get the possibility of some easy to implement flexibility for the humans.
I also believe that we should set some bare minimum level of civilization for those alternative cultures. In other words, avoiding tribes or stone age people (maybe opening an exception for, say, Mayans, that were quite advanced, though metal smiting was discovered very late for them).
Another possibility too would be to make the player's fort, though financed by their especific civilization, run by the guild, strengthening the idea of "merchant outpost". Then, if this is possible, with each civilization archetype, the player would get access to one or two special buildings (say, Huscarl Longhouse and Raiding Port for vikings) with special interactions and equipment.
Edit: I was thinking... I am pretty sure you can adjust a civilization to make sure it will bring only certain items. While it could be only certain types of drinks and pets, I think we could use it to implement a quite interesting system in which every civilization archetype will have a token, say, "Nordic Token", the only kind your home merchants would bring you. You buy them from the caravans, and use it to build the cultural building (you will have a list, but the token would be necessary, in the way that, as a Nordic fort, you can't get a Niponic building).
At the same time, that could be used in interactions a la Warlock to create fort members, maybe cultural warriors made as castes? That could be interesting, but given how valuable the tokens would be, it would be necessary for that warrior to be truly an elite soldier, but let's leave the balancing for later.