The following theory is not complete as there are some holes. I also believe that there is more than one conflict taking place on the island; but my thinking is Life versus Death is probably the major conflict. If this has already been explored, please forgive me.
I believe the Light versus Dark John describes in S1 is a conflict between Life and Death. I think Jacob represents the Light (Life) and MIB represents the Dark (Death). I think both are necessary and cannot exist without one another. So how does this conflict fit into the Lost equation? Let's explore some of the remaining characters to see how they fit into this theory.
Jacob: He appears to be ageless so he is constantly opposed to death. Because he represents life, he cannot truly die as long a soul remains on Earth. So what is Jacob's agenda? I believe he wants everyone to have an opportunity to fulfill a meaningful life. Because a "meaningful life" will vary from person to person, everyone gets to choose his or her own through free will. Those who embrace and appreciate life and do not take it for granted are probably held in the highest regard. Those who do not fully appreciate life given are sometimes given an opportunity to "cheat" death in hopes that it will make their lives more meaningful. In short, Jacob manipulates the living to aspire them to live more meaningful lives before their eventual death.
MIB: I am not sure if he is ageless, but he could be if he is supposed to be Jacob's opposite. We don't know much about him, but my hunch is he represents death. So, what is his agenda? He believes people are consistently engaged in conflicts that result in death. Sometimes, through Jacob's influence, people may elude or "cheat" death which angers MIB because death is the ultimate destiny for everyone. Jacob tries to convince MIB that life does not always end the same way (meaningless), it only ends once. Everything that happens before that is just progress. MIB disagrees and aims to prove otherwise. In short, MIB manipulates the dead to create conflict and death among the living.
Jack: Since Jack is a doctor, he is in a unique position in the Life versus Death conflict and that's why he is probably the main character of the show (and the leader of the Losties). Jack has saved and not saved lives on and off the island. Interestingly, he has saved at least 1 life he thought he could not, and did not save a life he thought he could. In no other person does this conflict exist more than Jack because his work requires him to make life and death decisions. But even the best surgeons cannot consistently "cheat" death. In short, Jack's primary purpose is to save lives and that make him an enemy of MIB.
Locke: He is a character that has cheated death on many occasions. He crashed on an island, was pushed out of a window, fell down a well and was shot in the abdomen. Even his survival at birth was a longshot (I think he was born premature). So on one hand he appears to be given many opportunities (by Jacob) to appreciate the life he was given. Instead of embracing his life and living it meaningfully through free will and choice, he is consumed by his destiny. Destiny for the purpose of the show seems to be death, so Locke for all intents and purposes is on a death wish. In short, Locke is the antithesis of life and therefore an enemy of Jacob.
Smoke Monster: I believe Ole Smokey is the "Grim Reaper" of Lost. It's purpose? Smokey travels from person to person trying to find out if that individual proves MIB's point that "it always ends the same" with people. If the individual has proven he or she is a ruthless killer with no redeeming qualities and is not apologetic for lives taken, MIB's point about mankind has been proven and that person's time is up (e,g, Eko, Freighties). If the individual has some contrition for past actions, he or she is probably spared (e,g, Ben). In short, Smokey is a judge to determine if MIB's opinion of people is correct.
Desmond: At first, Desmond led a purposeless life with little direction. He finally found a purpose...his destiny was to defeat Widmore in a race to earn his respect. His consumption with destiny left him being stranded on an island. He was relegated to pushing a button every 108 minutes. He contemplated suicide and then survived the blast when he turn the fail safe in the hatch. Desmond cheated death. He even developed the ability to predict Charlie's death and subsequently helped Charlie cheat death. In addition, Desmond was willing to perform a selfless act in offering to go underwater to the Looking Glass to spare Charlie yet again. Desmond now appreciates life and has procreated. In short, I believe Desmond is an ally of Jacob and enemy of MIB.
Ben: He claims to be an emissary of Jacob, but his actions are in stark contrast. I am not sure anyone on Lost has killed more people on and off island as Ben. He did seem contrite when his daughter was killed and for once took responsibility for a death. Smokey allowed him to live in an attempt at possible redemption. However, I think he "killed" his chance of redemption when he stabbed Jacob repeatedly in the chest. The next time he sees Smokey, he's a goner. In short, enemy of Jacob, ally of MIB.
Sayid: He has been a torturer and a murderer. Even as a child he had a penchant for killing. He tortured Saywer to get medication for Shannon. He killed ruthlessly for Ben off island. He even tried to kill a young Ben on island. At this point, it would seem like Sayid is a poster child for everything MIB believes in. Death follows Sayid. However, Sayid assists Jack in detonating Jughead even at the possible expense of his own life. In short, his selfless act may be too much to forgive thus making him an adversary of MIB.
There are other characters left to be explored, but I will summarize here: MIB wants to kill Jacob, because that's what death does...end lives. Jacob, being the representative of life, wants to see people lead meaningful lives. He wants people to value their life and the lives of others. The conflict between the two leads to war. The island provides an interesting battleground because it can probably grant people an ageless (not eternal because they can be killed) life on island if they prove to be worthy (like Richard perhaps). MIB does not want more people brought to the island because of the possibility it may lead to more ageless people living there.
Life versus Death and an imminent war to follow. The tagline for Lost, "Destiny Found", might as well have read Death Found. Well, as far as my theory is concerned anyway.