Freelancer/WMG

The cloaking technology from Starlancer wasn't lost.
Sometime during the war, one side or the other developed a radical new kind of sensor that could see through cloaking fields. As it was also superior to previous sensors in other respects, it soon became dominant. Nobody has managed to figure out a way to completely negate it, and cloaking devices became useless.

Freelancer/Starlancer is set in an alternate Star Trek timeline.
The Eastern Coalition exists in both universe. It's WILD Mass Guessing for a reason.

are an early form of the Reapers
. They just don't look mechanical yet.
 * Probably jossed:
 * are not Reapers, but they were created/enslaved by them, like the Keepers or the Collectors. The Reapers have a base in the Sirius System (or it is important in some other way) and use them to keep other species away. The five ships that brought the colonists there left before the protheon ruins were found on Mars, thats why humans there have no mass effect drives.

President Jacobi knew/ordered/intended for The Order to attack the Donau
Rheinland was the one who found the alien artefacts a few months ago, it was how the Nomads infected much of Rheinland including the Chancellor. It was that point Rheinland was getting aggressive and therefore Jacobi saw the visit from Admiral Schultzky as a threat. This could also be why the president was planning to ban illegal artefacts in Liberty.
 * While it's very likely that Shultzky was infested and that is why he was killed by the Order, it is very unlikely that the President had anything to do with the Order at that point. As for the banning of artifact trading, that most likely done of the advice of the other high ranking Liberty officials who had already been infested. The Nomads are supposedly the guardians of the Dom'Kavash ruins and artifacts and as such are attempting to stop their trade and recover them. This is why both of the most deeply infiltrated colonies have not only banned the trade of artifacts, but are also working to seize them from those already in possession of them.

Samura feeds their fish farms with alien organisms inundated with Cardamine

 * In some news reports and rumors, I heard that people that ate or were exposed to the seafood Samura raised on Junyo became sick sometime afterward. When they get more, or when they set foot on Junyo or Kurile, the planet where they cultivate the alien organisms they use as fish feed, they suddenly recover. Oddly enough, the symptoms are very similar to that of Cardamine withdrawal. Since the Alien Organisms that Samura feeds their fish originate from the same part of Sirius as Cardamine, the Edge Nebula, could there be a connection to the addictive drug?
 * Assuming that Cardimine is an organic compound like most drugs and is produced by the life on planet Malta as opposed to being some sort of inorganic compound that is simply part of the planet's make up, this could mean that the alien organisms are actually the source of life on Malta. i.e. Life on Malta was originally seeded by a meteor containing these same organisms.

The Dom'Kavash were wiped out by the Shivans.

 * Not many people know this, but according to a rumor I heard at Pueblo Station, Ageira Technologies had developed the Jump Gates from a Dom'Kavash Jump Gate relic found on Planet Manhatten. The Jump Gates, as well as the Jump Holes and the Alien Jump Gate used late in the game, function in a similar manner to Subspace Jump Nodes, even moreso in the case of the Jump Holes. If the Dom'Kavash Jump Gates used Subspace to function, they might have caught the attention of the Shivans, who are known to be sensitive to Subspace travel, and invite them to attack. Since the same technology behind the Alien Jump Gates is used by the gates developed by Ageira, the Shivans might return to exterminate the Terran colonies in the Sirius Sector.

The Corsairs are preparing for a war with the Colonies.

 * The Corsairs are the largest criminal organization in Sirius, and according to a story found on the news at the Planet Crete bar, they are getting ready for a full-scale invasion of Rheinland. They plan to eliminate the Red Hessians, and then capture their headquarters in Dresden to use as a staging ground for the Rheinland attack. Judging from their superior numbers and equipment, it is very likely that they will decimate Rheinland. Their economy has suffered since the GMG defeated them in the 80-Year War, which had also cost them their entire starfleet. Once the pirates conquer Rheinland, they will move on to invade Bretonia, Liberty and Kusari.
 * Add that to the beating they suffered by being The Nomad's whipping boys, and the fact that said Organic Security System will probably be looking for another puppet to use against human space, and.... HmmmmmH!
 * Actually, the 80-Year War did not cost Rheinland its entire starfleet (and even if it had done, decades passed between the fall of the Empire and the start of the game). That isn't really relevant, though, since the Nomad War almost did (they have a single battleship left, and an old, run-down one, at that). There are other problems with the plan, though. To begin with, the Corsairs' military may have superior numbers to Rheinland's, but there are more Rheinlanders, and groups like the Bundschuh are likely to rally 'round the flag in a time of crisis. Then there is the question of how the other colonies would react to a full-scale Corsair invasion of Rheinland space. At least Bretonia would be inclined to support Rheinland (Bretonia and the Corsairs already are clashing) early on, and if the Corsairs actually manages to win against Rheinland... and then there is the Outcasts, who hate their Hispanian brothers about as much as they hate the Colonies, to consider. Now, that they might overcome... but actually invading the other Houses as well, after they inevitable suffer damages in conquering Rheinland and has to divert forces to keep Rheinland down? There is a phrase for that, and it is Suicidal Overconfidence.

So, what were the three other ships the Alliance built?
According to the Outcasts, the Alliance actually built eight sleeper ships, not five. Three were destroyed by the Coalition fleet. So who were the others, and what were their names?
 * France is probably the most obvious candidate. In Starlancer, they did actually have one known ship and squadron survive. Possible names would be the Gallia or Aquitaine.
 * Italy is another. There was one surviving Italian squadron, and presumably unnamed Italian ships (not to mention civilians). Dunno what their name would have been.
 * Israel is a possibility. Israel is never mentioned in the first game, so its status is unknown - for all we know, it joined the Middle Eastern faction of the Coalition. However, if there was an Israeli sleeper ship, there's an obvious name: the Zion.
 * Any number of former British colonies - those that didn't get stuck on the Bretonia. Three possibilities come to mind:
 * India. If it didn't join the Coalition, India would probably have a ship, maybe the Hindi or Mughal. However, if India was a member of the Alliance, it almost certainly would have fielded warships, so it probably did join the Coalition.
 * Australia (and possibly New Zealand). Geographically distinct enough. Uluru might be a good ship name.
 * South Africa (and possibly the rest of southern Africa). We know South Africa was a member of the Alliance (one of your fellow pilots is South African). Their ship could have drawn its name from any African tribe - the Bantu, Zulu, or Xhosa, for example.

Most of the houses are only selling "monkey models" of their fighters
Think about it, the Defenders and Patriots that you can buy are outgunned by Liberty Navy fighters of the same type later in the game, as well as several other ships in the game completely outperform them. This is likely also true of Bretonian and Kusari ships. Rheinland however, may well be selling full-power military fighters to pay off their massive war debt.

Freelancer is an alternate future timeline of Starlancer
In Starlancer the player (if they managed to get best results) manages to become the Alliance best fighter ace, who squadron manages to save the Alliance from destruction and even turn the fortune of the war against the Collation, liberating the outer planets collanies of the Solar System and may of been on their way to liberating the inner solar system. Yet the Prolouge of Freelance seems to ignore this and shows the Alliance barely holding out in Pluto buying enough time to build generational ships that would be sent to another star system. In my view I think Freelance Prolouge is where the player got killed fairly early in Starlancer as a result the war never turned in the Alliance favour