Since everyone seems to enjoy pointing out a "plot hole" that was fixed a long time ago and it seems nobody else in the team saw fit to mention it. I've just been lurking mostly, but I finally decided to pop in long enough to clear this up (and hopefully increase the amount of helpful comments we get in here):
Cythera is in the same system as New Terra (probably the next planet over). The Conestoga, though advanced, wasn't so much limited by available resources - after all, they had an entire, resource-rich planet at their disposal, not a barren rock like New Terra.
Then, while the Conestoga is in orbit around the hydrogen mine at Jupiter (as per Outpost 1), they put their 2 contingency plans into effect. First, they launch a nuclear warhead at the asteroid, attempting to divert it. This fails, instead breaking it into 2. They quickly cobble together a second starship, thinking that its chances of survival are basically nil but they may as well try.
They launch the Frontier at the same time as the Conestoga leaves Jupiter. This is where the plot hole is filled in - the nuke they launched not only broke apart the asteroid, but also released a massive EMP wave (which would normally not travel TOO far, but in space there is less particles in the way to block it and it travels for quite a ways) which scrambled the Frontier's navigation and comm systems.
Unable to plot a course or communicate with the Conestoga or Earth, the Frontier Savants simply decide to follow Conestoga and land wherever they land. This gets scrapped when they reach New Terra's system. The Frontier is caught on the fringe of a cloud of space debris (the same cloud that causes the meteor showers on New Terra) and loses track of the Conestoga, and they decide to land on Cythera, seeing that the meteor storm is inbound and will probably cause great difficulties to survival on NT.
Several years passed, and the Phoenix Voyager was launched from New Terra, intending to go to another system. The rushed starship program however resulted in a problem with the ion drive module, which they needed for a long range space voyage. They are forced to land somewhere closer, and decide on Cythera.
Hope that clears things up for you guys!
P.S. OP3 IS NOT DEAD!!!!! we're working on recruiting more people to help us with programming (anyone who's willing to lend a hand instead of demanding we give it up would be most appreciated). This project isn't dead, and it might take awhile, but IT WILL GET DONE. Not a one of us is going to admit defeat, now or ever. [/finality]