I would definitely like to see some kind of AI enemy that shares the universe with us. The "AIs" could be player designed ships or bases that have been abandoned for a long period of time driving the ship's AI to malfunction with catastrophic consequences. They would be hostile to everything organic and squishy so it gives the players that want to be moral a way to experience combat and boarding without needing to harm other players. Eventually there could even be fleets of these ship traveling through the universe like some kind of cosmic natural disaster to anyone that can't properly defend themselves. To stop this force of nature a military Org with sufficient firepower could be hired to deal with them, in other words a Raid created by players and destroyed by players. The frequency of these raids will be rare due to the method in which they are created, but if this process is too slow the Devs could implement the ability for AIs to capture the ships of their fallen enemies.
I know the Machine vs Creator card isn't the most original concept in Sci-fi, but I really think that this could be a good fit i Dual Universe since it would all be player-made, it gives purpose to an Org's military that isn't the small threat of pirate attacks or the full-scale Org v Org war.
Let me know what you think about this topic, I'd love to flesh this out a bit more.