I would like to see 2 features in some future version of the game:
1. Mines: (as in the explosive kinds you don't want to run a ship into). There could be different levels that require more research to detect and sweep. Perhaps allies could be allowed to see them too. They could be used to block off sections of space for defensive purposes or could be placed along enemy trade routes to disrupt traffic. A possible idea in addition would be to give races a random chance of discovering who placed a mine if they run into one.
2. Stealth: This would allow two new technology trees, one for stealth and one for detecting other ships. Players could then ambush ships in a time of war like Wolf Packs or covertly slip into enemy territory for scouting purposes. I would think that the cost of "cloaking" a large ship would be a lot more (either in BC or in space consumed on a ship) for large vessels than small ones. It could also set up strategies like making one ship, planet, or base look like easy prey with a cloaked vessel or fleet waiting near by to ambush anyone taking the bait.