The Wormhole wrote:
Actually, the Eli remaining was how the ending was re-written after they got the cancellation word. The original ending to the episode, had they believed the show were going to continue would have had everyone in stasis except for Young and Rush. The two would agree to a coin toss to decide who would go into stasis and who would remain outside. The episode would have ended with the result of the toss not being revealed, thus being the cliffhanger.
Looks like that idea was only a pitch, not something that was dropped due to cancellation.
As for the Destiny crew not making it home, I figured that Rush would have been the only one who didn't make it. I think he would have found whatever he was looking for which didn't include going home.