When the initial miniseries aired I dictated my ideas on how it could have been better. Time has proved I was wrong and I've been amazed at the quality of the show since. That won't stop me from opining again and the season 3 premier seems like a good place to chime in once again.
I just saw missed opportunity after missed opportunity.
3.1 First thing they should have done after that season 2 cliffhanger is get us away from New Caprica and leave us wondering. The show is called Battlestar Galactica and to be honest the happenings on the battlestars were pretty dull stuff. They should have spent an episode based around the battlestars and the fleet. Something along the lines of the first seasons Episode 33 with the Cylons chasing and pushing the now lax and understaffed battlestars in the hopes of ending resistance. Eventually this would lead to the fleet breaking up with the Galactica taking the rag-tag civilians in one direction and the Pegasus trying to draw the Cyclons away. The Pegasus jumps close to find out what's going on down on New Caprica, then when chased away they try to threaten the regeneration ship again. The episode would end with the Pegasus coming across a Colonial Frigate. A small warship from Gimini that has survived.
3.2 Second episode has to be the Baltar episode. He's basically used up as a character now. Something needs to be done or he'll just be shot as soon as the storyline leads beyond New Caprica. He should try to run the occupation. Fighting with Roseland and Tom Zarek over what to do. Baltar wants to build New Caprica, make life better for the folks and they'll stop fighting. Zarek doesn't want any part of collaboration. Baltar eventually orders Zarek's capture which leads the man to join the underground (which clearly he has already had some connection to). This should be juxtaposed with scenes of a clean cut, short-haired Baltar ruling over a peaceful modern planet (is it another insane dream of his?). Terrorists led by Zarek followers try to disrupt the peace constantly and clean-cut Baltar eventually imposes some brutal measures. Terrorists attacks on New Caprica continue and the Cylons talk about plan B, eventually arresting Baltar.
3.3 Third episode is the resistance. Why blow up Cylons when they just regenerate? The humans have only so many people so is suicide bombing even a worthwhile tactic. This would get really touchy when Tom Zarek joins and a lot of his formal colonists join with him. Zarek wants to have the rebels join the police force, take it over from within, convince the Cylons its peaceful enough that they leave on their own. Tigh wants bloodshed. They've gotten word from Pegasus that they are being chased, they need to kill enough Cylons that the damn Resurrection ship can't leave orbit. The two sides part and conflict with each other. Tighs wife turns over info on Zarek's folks that gets his plan disrupted and convinces the Cylons to bring in a new force. The end of this episode would introduce the short haired clean-cut Baltar, called Baltar Mark 2 for now, has been running Gemini (or whatever Tom Zarek's homeworld was) since the days of the initial attack. He helped Gemini avoid the holocaust and has been fighting against Zarek's old terrorist buddies ever since. Baltar Mark 2 has brought many of his followers to help dominate the humans on New Caprica. They feel that they can live with the Cylons if the violence stops and they are willing to be brutal to do so.
This opens up a huge number of opportunities. Does the fleet try to blow up the regeneration ship again? Do they try to help an uprising on Gemini. Perhaps the original colonies are nearly unprotected by the Cylons and the fleet (or Pegasus alone) could attempt multiple rescue operations. Perhaps under fire, perhaps not. The metaphor on suicide bombings and collaboration are stronger if we have more humans and more likely collaborators.
The resistance now has much more of an excuse to use suicide bombing because the collaborators are not human in their eyes. Word of a surviving colony screws with morale because many are willing to live under Cyclon occupation on Gemini rather than go on living in mud and fear. Some of the colonists from other colonies start to blame the Capricans (who have pretty much led humanity so far) for their ills and start to side with Tom Zarek. This creates serious support problems for the resistance and moves Zarek into much more of a position of power (to replace Baltar to some extent when they move beyond New Caprica).
The Cylons themselves debate transporting the docile humans back to Gemini and then erasing the remaining humans on New Caprica. And of course that destroy the Pegasus came across turns out to be full of collaborators who lead the Pegasus into a trap.
That's how I would have done it. It would have tweaked the terrorism vs freedom fighter allegory more and opened up a whole bunch of new possibilities and cliff-hangers. Perhaps Ron Moore's team will surprise me again and a year from now I'll reread this and think I was naive not to trust them. But for now those are my thoughts.