The population of millions on Novus was supposedly descended from a small handful of people from the duplicated Destiny crew. That's too small a gene pool and many recessive disorders would show up, as a consequence of the inbreeding. On the other hand, it may be that there was a high mortality rate and those that survived were free of such genetic disorders. This has happened on Earth, in small, isolated communities, as on (for example) Tristan da Cunha. (There, the population of 238 shares only eight surnames but there are no genetic disorders, in spite of the inevitable inbreeding.)
Eli and some of the others remain on the planet saying that the longer they wait the more data they can upload. There is no reason for them to stay once it's started; all they're doing is watching a progress bar.