I find it ironic how over-emphasized Space combat is and Ground Combat is so neglected. I really enjoy the PVE Ground Missions, and I wish we could see more of that in Sector Space. Much like the current Enemy Signal Contacts, as a way to mix up the Defend -insert Sector Block- Missions.
One way you could implement this, is the bad guys somehow beamed aboard your ship, so you have to fight them off, or vice versa. Bonuses for Engineers with Boarding Party abilities.