We're adding additional loot drops to all high-rank NPCs. This includes Captains on the Ground, and Battleships and Dreadnaughts in Space. All of these NPCs will now have a very high chance (I believe it's 80%+) of dropping a green-or-better piece of level-appropriate gear.
Given the number of high-rank enemies you face in an average STF, you should end up walking away with a good haul of decent-to-wonderful loot to either equip, or sell for EC.
These changes were just made this week, and didn't make it into this morning's maintenance cycle. It's likely they will show up next week, though they may stir on Tribble for a bit before coming to Holodeck.
Cryptic - Systems Design