Edit: Download link changed to the 0.8.3 download, change log in the link.
Some information on the more unusual features. Spoiler alert, I'm going to explain the Tarellian Plague, in detail.
On random maps, there are neutral factions that can spawn. These neutral factions can send out raiding parties to attack other worlds, and will rebuild their lost fleets until taken out. These factions also have starbases that can be captured and used to gain additional assets, with the appropriate research.
These factions are the Maquis, Talarians, Tamarians, Ferengi, and Son'a.
Further, there is the House of Duras, which potentially will grant a minor boost to ships that visit the planet should you defeat them.
X Class Worlds
These are planets with extremely hazardous features. By virtue of an absurdly complicated buff chain, these planets will progress towards one of several outcomes, that trigger based on various conditions. One such outcome is to have a Crystalline Entity visit the world some time after it's colonized. Another is a Tribble infestation, which will spread like a disease through the fleet and along trade routes, seriously hindering some aspects, while improving trade, as they're a highly marketable pest. The Klingons suffer the worst from this one as they hate tribbles, but they eventually exterminate the pests aboard their ships. Infected ships can also transfer their problem to enemy ships that lose their shields.
Unlike the pacts in vanilla Sins, SOA2 pacts are based around subjects of research. Gaining a pact with another faction grants you access to a unique technology that can be researched. This can do anything from give a general boost to ships, to improve a specific ability on a specific ship, or grant a new ability entirely.
The Tarellian Plague
As of this version, SOA2 has a new random event. This spawns a Tarellian Starship, shown above. This is a slow moving, fragile vessel, that will, upon reaching an inhabited planet, infect it with the Tarellian Plague. This plague will eventually wipe out life on the planet, and can be transmitted to ships in orbit at random. The impact of the plague, and the frequency with which it is transmitted, increases over time.
Upon transmission to a ship, one of two things will happen depending on what kind of ship it is. If it is a military ship, it will slowly degrade in performance and suffer damage at random, from accidents resulting from no maintenance as the crew sickens and dies, and eventually it will explode. If it is instead a trade ship, it will eventually destroy the ship, but has a chance to infect any new worlds it visits before it is lost. This new case of the plague will be just as dangerous as the original, further spreading the disease should you fail to take steps to keep trade from passing through.