Yea i would say its going to get more advanced, but not any more complicated. ( ideally simpiler, without degrading choices )
I don't think we will ever be adding in explicit faction features. by that i mean we're avoiding having some menu where you have to declare your affiliation. We'll eventually be adding some character customization (visuals) that people who want to consider themselves as a faction could use to color themselves. Things like having a pincode on a door or safe again you could share with your faction members. But we are purposely avoiding things like clan tag entry screens or some sort of built in to game faction system ( when it comes to players, npc's may be a different story ).. so that people and groups of people can choose how to identify eachother.
This also means that things like domination/conquest where you have to wait on a flag to capture a area or any other team based gameplay requiring a subset of game rules aren't planned. but for example if we allow people to upload their own image to be used for their own flags that they can craft and they then make a building and put their flags all over it, the natural thing to take over that building would be to remove the flags and optionally put in your own. I'm not saying we're going to add custom image uploading but using that as a example.
With that said we probably wont be adding tagging of people manually as well. It's not that were shooting for realism, but if you were able to tag someone as a friend and it showed [FRIEND] above their name (moreso if it did when far away but applies to close range as well), while its pretty common to see features like that in games today imo it breaks any survival instinct/fear. I personally think any means of identifying yourself or another player should be up to you and those who you want to identify you. Any outsider who is keen enough to be able to pick up on what you do between friends to identify each other (whether that means dressing similar, some combination of jumping and or 'secret door knock' ect) you will have to watch out for! Those kind of tactics are part of the game, by not putting in bullet proof ways to identify yourself, they are naturally there.
I like your ideas here, but there should at least be some way to have private chat channels that you can use to chat with allies/friends. Probably an invitation-only system would be good.