-Faster than Light Travel. This could be implemented in various ways, as a means of quickly traversing distances:
-Tachyon Drive: A drive powered by tachyon particles(For those who don't know, tachyon particles are theoretical particles that supposedly travel faster than light.
-Wormhole Generator: If you're thinking of implementing this, I recommend finding the book 'How to Build a time machine' from your local library, and looking for the wormhole section. To build a wormhole generator, you'd need items such as the Collider, Imploder, and Inflator. The book explains them in detail, but I'll give you a short summary here.
Collider: This is the device that collides particles(gold/uranium) together to create enormous amounts of heat(Up to ten trillion degrees), which pulverises protons and neutrons, creating 'quark-gluon' plasma, which is a substance in which quarks roam about freely. This substance must then be transported to:
The Imploder: To create a wormhole, you must bust a hole in spacetime, and to do this, you need a very very dense item. The substance from the collider is the first step. Then, the imploder uses a special magnetic field, along with explosions in a technique called 'Z-Pinch' to make the quark-gluon plasma much, much smaller, creating an object with a density of ten trillion trillion trillion trillion trillion trillion trillion trillion trillion kilograms per cubic metre. Yowza. This should create either a miniscule black hole, or a wormhole. Then comes:
The inflator: This device is what makes the wormhole big. Because currently, we have a wormhole that's tiny. 10^-20 times smaller than an atomic nucleus, in fact. The only way to make this big is to feed it negative energy, which produces antigravity. This antigravity will push the wormholes sides out, and make it big. If you choose to implement wormholes, tell me, and I'll give you the explanation for creating negative energy.
So now you have a large wormhole. This is still fairly useless, as the ends aren't very far apart. However, merely tow one end with you, place it where you like, and the two ends will be connected instantaneously. This may be a complicated process, but it's well worth it when previously 10+ minute(ingame) journey's become a brisk walk through the wormhole.
That's really the only two decent FTL things I can think of. If I come up with more, I'll inform you.
-Space Stations: Space Stations could be expanded into full blown mini-worlds, due to their almost guranteed enormous size. Friendly space stations, or hostile ones you plan on boarding could become enormous worlds, with auto-turrets, enemy marines, and other suprises to contend with. Or, in the case of friendlies, excellent opportunities to search out quests, supplies, and bussiness prospects.
Here's an idea I REALLY like:
-ALIEN space stations. And I'm not talking 'futuristic' aliens here, I'm talking about evolutionary Notrium-style aliens. Big fat blobs of living tissue specially bred for space travel, with aliens crawling all over them, a gigantic brain controlling them, and tentacles, poisons, and other nasties coming out of the very WALLS. Spaceborne spores, sent to colonize other worlds for the aliens, their own spacefaring alien hybrids. Boarding one would be like entering a nightmarish world of the surreal, with hidden dangers everywhere, and the possibility of surviellance through unknown means. I'd play your mod if all it had was alien 'spacecraft'.
Edit: Almost immediatly, I came up with still more ideas. Or at least one.
-Black Holes... as a weapon! Due to the unstopability of black holes, it's quite the force to be reckoned with. If one could create a few black holes, or find them, the gravity of the spaceship could be used to tow them around, like leading a donkey with a carrot. Plopping one into the pull of a planet, and it will fall straight through, going back and forth until it finally settled down in the centre. While this might be hard to implement, it could also be used against more susceptible things, like space stations, and spaceships, doing extreme damage, and being fully salvagable afterwards. Of course, it mightn't be so useful against moving enemies, but it could make a decent rearguard.