Superweapons, Moon Bases, & Covert Bases

Superweapons

What I really wanted for Endless Space 1 was late game options to help win the game aside the options (economy, supremacy, etc).

Superweapons are not a new idea but I think this can be incorporated into the questing chains being made for this game. For example, one doesn't simply research the superweapon and then construct it. I would love to see a questing and decision-based structure of events leading to the discovery of technologies and parameters needed to gain the weapons. There is so much room for ideas and what could be done with superweapons.

Weapons include: AI control (fleet distruption), Biological attacks, Nukes, Planet killers, Star killers, etc. Ideas for sci-fi superweapons are all in other games and movies that can be adopted into this game. Any unique weapons for each faction would be awesome.

Moon Bases

Again with ES1, I was hoping that moons played a bigger role in these games. Some moons in our solar system are almost as large as Earth. So, I would love to see moon bases or colonies added to give some systems an extra edge. Like some systems may have fewer planets to colonize but their moons may be just as valuable.

Covert Bases

Whether it is on a moon or planet, I would love to see secret installations be built across the galaxy that don't hold the same characteristics as colonization. Maybe these bases can be used to spy on enemy systems or help get superweapon tech. 

Bases could be made to establish long range trading posts or exploitation of resources without devoting your empire to populate the area with cities.

I guess I would like to see a change in the way colonization occurs. Because it is rather simple at the moment with incubating a system and the population then mass populates creating cities. Sometimes populations send out colonies and small posts for different purposes whether exploratory, resource, or military purposes.

Covert bases like the covert pirates you can hire to attack enemies add that depth in multiplayer when players are confronted with dynamic threats rather than fleets blockading systems.