The Stargate series as a whole has stayed away from any kind of philosophy but I do think that SGU had an objective of sorts it would've been nice to seen it played out.
I think Stargate made a very strong statement against false god's and I think eventually that turned into a statement against deities in general thus the Ori/Christian theme. Even though they avoided making comment on the Earth impact of all these false god's in real time consequences the Ori were clearly a statement against God and god's. It would have been interesting to see how the religions of the world would have reacted not just to the Gate program but the revelation than the religions of Earth were seeded by aliens and...evil...
Even though I'm Christian I think SGU would have been the perfect series to subtly plug anti deity themes to a stronger degree. Scott haveing a Catholic background, Wray being Lesbian. They really missed out on some good old fashion ideology conflict. Even the abortion thing with the baby. But with this huge revelation of what Destiny's mission was...that there was apparently evidence of a structure to the universe...come on...that's huge and could have been made epicly dramatic with the conflicts previously mention.
Really as far as my creative juices go...that's what SGU should have been about.
The cast should have been made of people with very different ideologies. Christian Muslim, Jew, Buddhism, Hindi and the secular ideology of nationalism and military or atheist.
Young should have been a military commander that was an uber American, "by the book or else" no room for interpretation, America is better than everyone else.
Rush as the Atheist would have been Absolutely AWESOME. I could see him playing the angry atheist role with the kind of solidarity that would have given Dawkins a run for his money.
Scott as the alter boy, later revealed as being molested by a priest.
Greer should have been Muslim. The natural clash here between him and Scott and Young would be obvious but not immediate. I would put him not just as Muslim but as a black Muslim.
Chloe as a Senator's daughter would be in cahoots
Wray as a lesbian feeding the liberal side. Eli should have been of Jewish decent, still a slacker genius. He would be an interesting balance (just as he was in the show between military and civilian) between religion and science. I'd imagine he and Rush would have the more interesting conversations. He could be the objective observer as everyone around him took their sides in certain conflicts. These ideological issues would be played against the "mortal coil" of survival and morality in survival. In the conflicts the big question would be asked and perhaps never answered.
Does might make right?
What is moral?
Is there a God?
What is the role of Science?
Should religion be band?
and don't stop there. Ask the political questions too.
Conservative and Liberals
Capitalism vs Communism (in fact I'm surprised there was no Russian or Chinesse on the crew)
And give us some insight in conflicts in other nations like Europe and Asia. It would have been a lot but I think it would have put SGU on the radar. It would have been Commentary in a way we'll likely never be able to speak about our reality...from a whole new perspective.