It's an episodic show, and MacFarlane said a while ago this season wouldn't have a cliffhanger or anything like that, so I wasn't expecting anything particularly different. Also, 13 episodes were made for this season, but only 12 were shown, because the last one would have been delayed because of Christmas etc, so it's been held back to air with next season. I don't know whether the episode that got held back was the 12th episode, or what was supposed to air as the last episode, so that may or may not have made a difference.
Very good episode btw. Definitely reminded me of Voyager - Blink of an Eye with the time acceleration and becoming part of the planet's belief system. Always an interesting story telling device. I think they covered the religious angle enough in other episodes to not need to do it here, but it was still fine here too, and left a more positive note.
I'm surprised a bunch of cavemen catching a quick glimpse of Kelly running away managed to capture such a perfect likely of not only her face, but the intricacies of a uniform completely alien to them.
Hopefully this means they're done with the romantic angle with the captain now. I understand wanting to include some drama for a more general audience, but it's run its course now, and the show doesn't need it. Also, I think they've managed to find the right balance of comedy/scifi now. I'm really looking forward to next season, and hope they get a decent run.