I believe that a way to keep things from getting cliquey is by giving every member an equal chance to impact the comm. Maybe let the plot decisions, such as who gets to be a special snowflake, be voted on and decided by the community instead of the mod(s). If you give the community more responsibility and input in how it is run, it becomes more personal to everyone in that community; besides, then no one tries to buddy up with the mod for special favors because the mod can't give anything special away without the comm's approval.
Another thing that might go well with this is rewarding individuals for interacting with everyone. Maybe in order to play a special snowflake character, players need to show their dedication to the game by getting a merit badge or thumbs up or another sign of approval from everyone else in the comm (or a vast majority). Of course, this could backfire into an even worse type of clique without the right management, so I'm not saying it's the answer. It is something I have seen done in rpgs outside of IJ, however, and sometimes it works. They could possibly be structured as challenges, such as write and complete a thread with every player in the comm for this shiny prize; something that could be completed by everyone, so there isn't undue competition beyond wanting to be the first to get it done.
I'm not sure what will get people to interact outside of their cliques, but I don't think it's enough to have a premise that says every person must like to write. People on this server hold grudges like we're playing for stakes way higher than rp, and they bring those grudges with them into comms. There needs to be something in place that encourages them to get over those grudges and discourages them from forming new ones against the other writers in the comm.