2010: Season 2: The crew goes into stasis while Eli stays behind to figure out how to get himself into stasis as well.
Series in Cancelled:
2019: Season 3:
They get the majority of the important actors back on board with the show. For all actors they couldn't, they are replaced by similar versions; besides the main crew a lot of the others aren't even memorable. Certain characters could also die do to faulty pods.
The gap in age:
At some point during the flight the ship has a malfunction affecting the systems of the stasis pods and/or there was some type of problem Rush and Eli didn't anticipate. This causes an issue where they age. Perhaps the ship has a process (a fallback option) where they are put into a medically induced coma, where an IV drip of essential nutrients was in those pods all along, and the ship automatically keeps them alive with it.
Or perhaps Eli figures out a way where they can only dial out from earth to Destiny (1 way connection). So they can send food over but not gate to earth. And earth never sends any new characters over since it's a one way trip. The crew then lives out their days on the ship. Nothing else really happens in the vastness of space. So a time gap without episode coverage makes sense.
To account for 9 years of space travel (or whatever is believable for the actors looking older):
Maybe things don't go exactly as planned and for some reason it takes longer. The flight could be 7-9 years (to account for actors aging); this is a long time, so maybe they opt to go in and out of medically induced stasis comas. The food supply for each pod conveniently only lasts for as long as they need it, so by the time they get to the next galaxy they are hungry and out of luck again.
The adventure continues...
SGU had such potential with the origins/fingerprints of the universe plot. It would be a shame, albeit much easier, to create an entirely new show and not continue this one.
It will never happen but I wish it would.