I doubt it will be the way it goes in the first season.

It MAY be the ultimate conclusion of SGU... or the way they might get the teams back to earth is via the ancient coms terminal and then downloaded into new 'brain dead bodies' or replicator made forms using atlantis tech as atm it's still on earth.
Aside from speculating about an ending to the season or the show... I have to say in regards to the show itself..
well. It's NOT the old format of stargate so I understand why a lot of people will struggle to grasp it. They have really made to their promise of making it far more personal, but where as so far I actually think SGU has been fairly reasonable on that front I do believe keeping it there is going to quickly become boring and the show is going to struggle. At the moment they've not done enough to rope in all the idiots with enough of a kick bang start off and their massive ability of overlooking the adventures within the ship itself is hindering my interest.
Ultimately we're there to watch Sci-fi and have some fun and enjoyment. SG-1 provided that. Atlantis had a good go but was a wasted plot... and if I really wanted to watch this sort of crap for any length of period i'd have tuned into BSG..which I thought was immensely rubbish despite all the hype surrounding it.
SGU needs to start balancing their episodes a bit more. There is a massive ancient ship.. yeah they have some resource problems but they cannot spend every second of every day applying to that without logically attending to the ship itself to explore and at least speculate it's systems potential uses...for all they know a botanical garden may exist!
The going to and from earth and desperately hopping on and off destiny for limited time on random planets is going to be worn down very quickly, though I have no idea how they're going to insure a reasonable and sustainable villain when they're travelling the universe although they could 'locate' one in a galaxy and face them as they travel through said galaxy.. if not bump into the Ori. I know the ori themselves are dead.. but that's not to say they wont still have adamant followers out there and we don't currently know where they're galaxy is and further more the replicators were hopping around in space for millennia, another potential resurrection lies there.
On another point I am thinking a 'Die Hard' map may be applied to a fair few episodes. A villainous force taking over destiny for nefarious purposes.. the source of which coming from without or within...any atlantis, spoiler aware, fans will already have noticed we have our new female actress played Acastus Kolya named and the plot pointed out.
I think it's still too early days to come to an utter conclusion of SGU.. i'll wait until the end of the season before I make my final judgement.
I do however enjoy watching Ely, Scott, Everett, TJ and Rush.. I think they're very good characters for their own reasons at the moment. (some of the girls are hot too, but i've not been able to click with many as actual characters yet..even Senator's daughter or dark haired officer).
on a side note. if you need any information regarding the ancients I wrote up their history on these forums. It's in the ancient/asgard section.
Accolades/Titles:
Started Playing: April 2005
Honours (5): Hall of Fame 2009. Annual Awards Host 2008, 2009, 2013, 2014 and 2015.
Winner (12): RP'er of the Year 2008, Runner Up Poster of the Year 2008, Debater of the Year 2008, War of the Year 2008, Poster of the Year 2009, Alliance of the Year 2009 (Nemesis Sect, Creator), Alliance War of the Year 2009 (Nempire vs Mayhem, Instigator), RP'er Runner Up 2009, Knew You'd Be Back 2010, Conflict of the Decade (FUALL v TF), Conflict of the Decade Runner Up (Ga vs TF), Alliance of the Decade (TDD).
Nominated (8): Writer of the year 2007, Avatar of the Year 2007, Poster of the Year 2007, Villain of the Year 2008, Player Sig 2008, Race Player of the Year 2009, Most Missed 2010, Alliance Leadership 2010, Most Missed 2011.
Commands (3): Supreme System Lord 2008, 2010, 2011 and 2012. System Lord Council 2006 - present. Dark Lord and Emperor of the Nempire 2009 - 2011.
Alliances (9): DDE, EA, OSL, TFUR, DDEII, AI, RM, WoB, Nemesis.
Forum Roles (4): Former Misc GM, Race Mod (Goa'uld), Debate forum patriarch and mod.