Haven't done Ryujin yet myself, but I hear it's great. Supposedly lots of covert stealth stuff. I personally also enjoyed the Freestar Rangers quest. It's got more political intrigue than the others I've done. (Also leads you to the Porrima system, which has one of the more interesting and bigger sidequests in it.)

One compliment I will also give the factions as a whole is that you don't immediately become the leader or second in command. Hell, you stay a Deputy until the end of the Rangers quest and only then become a full ranger. It actually feels like an earned promotion.