I was thinking maybe the Remnant should have the ability to cloak one of their ships or maybe an area within a system. As this was not widespread and could potentially unbalance the game it would have to be prohibitively expensive to research or activate this ability.
You could also make it so that they have the ability to recover lost imperial technology of some kind when they take back a world from an appropriate faction like the New Republic or the Warlords. Again this would have to be balanced by making it so that this only occurs on certain specific worlds or has a low chance of actually occurring.
Those are a few ideas I had, hopefully they help. Keep up all your great work