My theory from last week still seems to be holding up with the new episode, The Substitute.
Smokey is all dead people and seeks the destruction of the world (and all life), while Jacob is associated with life and particularly babies.
In The Substitute we learned that Jacob is searching for his replacement and that there are six candidates for that job, each of which is represented by one of The Numbers. Smokey’s game is to get all 6 off the Island and to kill Jacob and then he will succeed at destroying the world. We’ve been told in the past that The Numbers are related to the destruction of the world and now we are starting to learn how.
Smokey was close to getting them all off with the freighter. He managed to get Jack, Hurley, baby Kwon (I’ll bet it’s the baby, not Sun or Jin who is the candidate), and Sayid off in the helicopter. He tricked Locke to leave by posing as Christian (remember, Smokey is all dead people we see on the Island) in the cabin and by the wheel to convince Locke to move the Island and be transported off the Island. If Sawyer hadn’t jumped from the helicopter we would have had all six off the Island, could have killed Jacob through Ben, and would have destroyed the world.
Interestingly, sacrifice and suffering are essential to keeping the 6 on the Island. That is, life requires sacrifice and suffering. Sawyer sacrificed to stay. And we see in the flash sideways that everyone’s suffering is getting resolved. Locke comes to terms with his disability. He has good relations with his dad, who is coming to his wedding. He’s getting married to Helen. Hurley has good luck in the parallel world. Kate is innocent. We can see what the world would be for them if they were never drawn to Island and it looks pretty good. But their personal happiness is associated with global destruction.
And when Jacob visited each of the 6, he ensured the suffering that would draw them to the Island. He brought Locke back from death so that he would be disabled, futiley go to Australia for a walkabout, and end up on flight. He gave Sawyer a pen so that he would write his ledge to kill the man responsible for his parents’ deaths. That quest drew Sawyer to Australia and onto the flight. Kate was saved from being caught for shoplifting by Jacob. If she had been caught at that young age, maybe she would not have been always on the run and ultimately a murderer.
Even though Smokey represents death his appeals are seductive, especially to people suffering. Sawyer’s current gloom is precisely what makes him vulnerable to Smokey’s attempts to get him off the Island.
Over the rest of this last season, each of the six will die or leave the Island. But baby Kwon will save the day because she is really the candidate, not Sun or Jin. And she and baby Aaron (who now appears to be on the Island with Claire) will somehow become the Adam and Eve in the cave.
Jay P. Greene's Blog 
I bet it isn’t Smokey’s intention to destroy the world. This is the 21st century and writers and viewers are more sophisticated than that to allow such a one dimension bad guy.
I bet he just wants to get off the island because he is trapped, like he says. He’s trapped in a never ending loop that will only end when he dies. If he leaves the island, the people on the island die.
However, the island needs special people on it to survive. The only way Mr. Dark and Mr. Light can end their time traveling loop is to find themselves a replacement – and by replacement, it probably means Mr. Dark and Mr. Light die anyway.
They’ve probably lived through the loop a dozen times over. Maybe Mr. Dark and Mr. Light even bounce through time themselves.
I think you’re right Patrick. When Smokey says he is trapped, I bet you are right that he is trapped in repeating life. Essentially, he wants to die. This will have bad consequences for other people but perhaps that will fall short of ending the whole world.
You are also right that Lost will have to complicate things to make Smokey not seem so bad. They’ll emphasize how Jacob manipulated everyone into suffering and coming to the Island. The 6 didn’t really have a choice in the matter. But then again one doesn’t really have a choice to become alive. Becoming dead can be a choice, but one has no say in being born.
I’d say by far the most important way in which Locke’s suffering is relieved in the flash sideways is that, with Rose’s help, he let’s go of his anger and accepts his condition.
Forgive my memory lapses:
1) When were the numbers connected to the destruction of the world?
2) What makes you say Kate is innocent in the flash sideways?
1) I believe it is in the orientation film about the need to push the button. Both Desmond and Locke believed that when they were pushing the button.
2) Kate says she is innocent. I know she may be lying, as per usual, but I’ll bet this time she is not.
She doesn’t say she’s innocent. She asks, “if I told you I was innocent, would you believe me?”