I love Galciv II. I have finished a few games so far and I would love to see these types of ships.
1. Stealth/Cloaking Ships.
Stealth ships would have the ability of being invisible on sensors. Cloak ships would be invisible on sensors and invisible visually. They would make great scouts that you could use to keep tabs on what your enemy is doing without having to worry about your ship being destroyed on sight. To balance these ships make then have little or no armament. That way you will not have a Cloaked fleet running around killing everything in sight. Perhaps limit them to a "small" hull size.
A tech improvement could be created where you can research different types of anti stealth sensors to put on your ships and starbases to detect stealth ships.
2. Q-Ships, Military ships hidden inside merchant hulls.
Imagine sending a ship to take out a freighter only to have the freighter shoot back and destroy your attacking ship. Would make attacking freighter traffic a little bit more interesting.
What do you guys think?