Ok, before you read this, you must understand that the plot below is original, Ok? I'm not so sure about the other ideas that are more generic, but tell me what you think!
(Note: This post may be a bit long for some of you, so bear with me here)
New plot:
The Terrans and the newly reformed Altarian Republic (Netro Mancer comes out of exile), and start looking for new planets to colonize. They come across a new civilization, the Tanortai Federation. Lets put it like this, the Tanortai are very intelligent dragons. They are not Humaniod. After sending a fleet to meet the Terrans and Altarians, The Terran Alliance and the Altarian Republic learn that the Tanortai have a new type of drive system, which the Terrans call Quantum-Bridge drive. It can allow ships to travel short distances in extremely short times. Where as a standard Hyperdrive would take a week to go to one star system, Quantum-Bridge would take an hour. The main down side is that each jump forces the drive to go into a recharge period. The longer the jump, the longer the recharge time. A ship could be recharging for months if it goes for enough. This allowed the Tanortai to expand in "steps". Despite its limitations Terran officers knew that Quantum-Bridge drive (QB) could be used for deadly hit-and-run attacks (warp one place, attack, warp somewhere else so they can't catch you). The Alliance and Republic exchange drive techs, and a diplomatic friendship begins. The Altarians are especially delighted at having these new friends around, because the Altarians and Tanortai have similar viewpoints on ethics and society (Both lean toward good and have techy societies), the Terrans are glad that have a new ally. For some time, the Tanortai help the Altarians liberte their worlds from the Drengin, who are still busy with the Korath (now called the Korath Consortium). However, instead of capturing worlds, some Tanortai actually build planets! This allowed them to literally build their empire. With this, the Tanortai create military outposts to help with the attacks.
Then the unthinkable happens. The Tanortai have reported that their technology to Hyperdrive has been stolen by an old ememy of the Tanortai, the Kolian Hegemony. This obscenely vile civilization, whose populations look like a mix between crabs and beetles, has captured a Hyperdrive equipped Tanortai ship, and has begun to use the tech in their own vessels. They then began to attack Tanortai and Altarian ships. The allies are quick to launch counter-attacks on the Kolians. They then learn that the Drengin Empire had forged a secret alliance with the Kolians, but did not share Hyperdrive. The allies also learn that the Kolians are building weapons that can tear chunks off of planets, killing the population, and create many new asteriod fields. This process can destroy the planet if it is small enough, though. Meanwhile, the Thalans decide that this is the year that the Terrans will destroy the galaxy, and also decide that the only way to stop the Terrans is to destroy them. Now, the galaxy faces yet another war. Each faction has powerful abilities. Who will win?
New Features that should be in the expansion:
Of course, the Tanortai and the Kolians!
Tanortai Federation Super Ability: Super Builder: Has factory bonuses and can build a ship to create a whole new planet (like Genesis, the higher the quality, the more expensive)
Kolian Hegemony Super Ability: Super Destroyer: Can build a huge ship that fires a projectile to tear off a chunk of a planet, killing everyone on the surface. Creates many asteriod fields. Destroys the planet if the class is below 8. The ship is used up when it fires.
Ship repair bays: Move ships into these and they will repair quickly.
Stellar cites: These hold many people and their populations should be able to grow. You can put shipyards and other modules on.
Quantum-Bridge drive: Read the plot story.
A Campaign: I didn't write all that up there for nothing!
Race trade goods: Each civilization starts the game holding monopolies on three unique trade goods. They can choose how much can be sold at one time. Selling more of the goods will make everybody friendlier with your civ, but you won't make as much money. If you don't make the products widely availible, you can make a lot more money, but you won't be as popular with the other civs.
Add the epic generator, I was looking forward to that in Dark Avatar.
Add voice acting, it would be neat to hear the other leaders talk. Have animations of them talking too.
Really improve ship battles. Right now, a two-person fighter looks huge next to a capital ship. Improve ship scaleing so that everythings looks the right size (20-person ships should be puny compared to 2000-person ships). When using free cam during fights, it zooms in and out really slowly, change it so you can zoom in quickly and get in the action (and take really good screenshots

)
Also, program ships so that their lasers face forward when shooting. Right now, they fire backwards when your ship is flying away. Another good idea is that when you zoom in close to a ship (with improved cam controls) you should hear a sound effect when it goes by.
Carriers: These have hanger modules onboard so that they can deploy fighter drones
Tactical combat: It is impossible for actual tactical to occur, since battles occur in three dimensions. You could just select a ship(s) from that list on the bottom left corner of the battle screen, and order into formations, and order them to attack certain ships. You should also be able to order a retreat.
Ship damage: Currently, ship damage is just electricity and smoke. During fights, pieces should be torn off. After the fight you would see holes and missing parts. Those parts would reappear over time (when the ship repairs)
Multiplayer: You know about that!

Make the good alignment have really good bonuses so its worth taking all those losses when you're colonizing planets.
Add different diplomacy options: Like 'do this or face war'. This you could use to keep people out of your civ's borders (those darn minor races, always hunting for resources in my turf

) You could also use it to explain why you went to war with another civ (You know, alliances, Super Organizers).
Remove the ability to build constructors for minor races. Right now, the fly around stealing resources and building starbases to expand their range. They shouldn't be able to do that or move around the entire map, being minor races.
Bump up the population growth rate. In Dread Lords version 1.0, growth rate went up fast, and made the game fun, then the updates and Dark Avatar came, and now population growth rate sucks. So, when setting up a new games, add a "base population growth chooser. The options would be like Dread Lords 1.0, which is fast, Dark Avatar, which is slow, and another option which is something in between.
Lastly, add some of the features from DA into DL, like asteriods and the enhanced graphics. Since Dark Avatar, I've had a hard time enjoying Dread Lords, because it didn't have what Dark Avatar has. So Galciv 2 developers, do everyone a favor!
Thanks for reading this. I appriciate it. Really. People, (including you Kryo), tell me what you think!