Will reputations become interconnected? Example: If I do missions for a "criminal" contact or mission giver will I automatically loose rep with the Advocacy or Crusade security?asked by ScryerVolt

Yes, there is a rudimentary version of the Enemies and Allies system in-game right now, but it isn't driving much content yet (You can see a bit of it with the Bounty Hunter guild gaining reputation when you do Bounty Hunter missions for other affiliated Orgs). We have plans to expand upon this system heavily.