I agree Reverend, there is the feel of course correction. Season 2 ended with the story going in definite directions and all of that was removed by the first 2 episodes. Last season we were expecting Rafe and Datak to begin an underground war against ERep. One episode in to season 3 and Rafe is dead, Erep is gone, Datak is on a totally different mission.
Lack of foreshadowing of the aliens is also a shame, especially since they don't really add anything other than supposedly bigger menace. We already had menaces. I do like the renegade Tak with his VC band because they live in a dangerous world full of factions. Coming up with a whole new alien/faction in the sky wasn't needed.
Still, looks great, totally enjoying it. I'd be curious to know what was behind the apparent jettisoning of last season's plot directions though.