Just read through the entire topic and its pretty awesome. Hope new people are welcomed. Loved the whole algae debacle. Since Im new I just wanted to say some things I thought up, see what people think without directing it as a sub-routine.
I really think the deep waters on Aquarius should probably be probed a bit. It seems the aliens have some knowledge of the solar system, so it wouldnt be odd to think they'd have sent out probes themselves, perhaps lost some on the planets. The discovery would be astounding! As for mining, why not go for planet C as well? It's got an abundance of metals, and would have ample amounts of oil and fossilised fuels due to all the animals. It was mentioned that some areas of the ocean were as shallow as 30 feet and relatively safe (compared to massive fishy), so why not take a note from DF and plug it/build a island and mine through? Some research would have to be thrown into construction but it could make for a safe base as well, except for crazy weather. Only predators would be flying creatures... in theory.
I also think that a contingincy plan should be consulted with the captain, in case of mass scale human death. Currently all humans are in one place which is dangerooouuus. Maybe have dna samples taken from all humans, and in case the human race is brought close to extinction (aliens, solar flare, meteor, riots) the AI can enact a plan to clone humans using the cloning center on Aquarius (modified of course).
And zomara, i really think you should add a set scouting group! Kind of a group of intel gatherers aimed more at the exploration of the solar-system/planets/astrological objects that can be used for the development of the colony. But kept seperate and away from the whole aliens thing.