[Sorry for the title, couldn't resist. Disclaimer: this is NOT the "best" theory.]
Absent fathers, bad fathers, well-meaning but ineffective fathers, patricide . . . Lost is a Freudian's dream, or nightmare. You don't need me to cite all the examples; they're everywhere. This theory posits that the "daddy" issues--in fact, the "parenting" issues--have their highest manifestation, and perhaps their cause, in the supernatural beings that inhabit the Island. Father (Jacob), holy ghost (Smokey), and son (little boy with blood on his hands): this trio probably isn't literally the Christian Holy Trinity, but they are all part of a single godlike entity that is struggling with bringing up its wayward child, humanity. A big part of the problem, the theory suggests, is that the positive influence of motherhood is lacking, or rather a "balanced" parenting team of father and mother.
If you thought Christian Shephard, Anthony Cooper, Wayne Janssen, Roger Linus, etc. were scary fathers, consider Jacob and Smokey. Jacob is the ultimate absent, or at least detached, father. The Others were his flock, but he refused to meet with anyone but Richard, and let his will be known in the form of obscure lists. Richard, we've learned, was kept completely in the dark about Jacob's plans--ultimately driving him to attempt suicide. Ben was so appalled by the suggestion that Jacob "didn't care" about Ben's sacrifices that Ben was unable to control his knife hand. Smokey, by contrast, isn't absent--unfortunately. He's there, he's extremely judgmental, and when he gets angry he demonstrates a wrath that could only be called Biblical. Nobody's going on fishing trips with the smoke monster.
I strongly doubt that Lost will turn out to be "simply" a Christian allegory, but the Christian tropes are undoubtedly there and can't be ignored. The "God/Satan" duality, I think, is a red herring--to have Jacob turn out to be "unambiguously good" and Smokey "unambiguously evil" would be too simplistic. Rather, I think the image of the Holy Trinity--God as three entities at the same time--will prove more apt. The third part of the trinity, the "son," I think has been mostly absent, primarily because humanity is the more important "son" in the story. But I will note that Flocke was very upset when he saw a vision of a little boy with blood on his hands. That's clearly another Island power, and I don't think it's Jacob, who has never been shown to shift shapes. I think it might be the third corner of the trinity, the son, who was sacrificed by dad in a manner recalling the sacrifice of Christ.
My point is, I think you can view Jacob and Smokey both as "fathers," or rather manifestations of the same father: they represent two parenting philosophies. Jacob is hands-off and wants children to learn from their own mistakes, even if they hurt themselves doing so--but he's rather unsupportive in the process. Smokey is hands-on and doesn't hesitate to punish transgressions, but he also has a more forthright notion of parenting: he's honest in his way, and he's not a fan of Jacob's vagueness and behind-the-scenes fate weaving. He also promises rewards for good behavior in a (seemingly) straightforward way.
This ties in rather neatly with the notion of the Holy Trinity. Christians believe that Jesus was sent to earth precisely to answer man's fears that God the Father was distant and uncaring. The "holy ghost" is often conceived as the wrathful, old-testament aspect of God, the proverbial "burning bush" or "pillar of smoke"--and if I need to point out the similarities to a "smoke monster," well, I've just done it, so never mind.
I don't want to dwell too deeply on the reasons I think humanity is the "child," because it would take up a lot of space. Hopefully, though, the exchange on the beach between Jacob and the Man in Black, in which Jacob appears to express faith in mankind while the MiB expresses strong doubts, is enough to validate the paradigm.
Now, one could easily take this structure to imply that a Christ-like "sacrifice" will lead to resolution and redemption. That strikes me as a bit too facile. The notion of "sacrifice" is indeed deeply embedded in the Lost mythology, and I do think it will prove to be the single most important factor in the resolution, but I believe many people will be called on to make sacrifices, big and small (and we've seen many examples of this already). Jacob has already done his part by "dying" for the cause (although he lives on, for all intents and purposes), making him Christlike in his own way. What I want to suggest is a little more controversial, and a little more left-field: that "motherhood" holds another key.
The Island is also the locus of dysfunctional motherhood. A "plague" was unleashed that kills women giving birth on the Island. Claire was snatched and "treated" without genuine consent because of her pregnancy, and it was suggested that she was going to be opened and sacrificed to save the child. To Sun, pregnancy meant either losing her husband or a death sentence. Eloise Hawking killed her son, Daniel Faraday, on Island soil. However, I don't necessarily see these patterns as indicating competing "philosophies" of motherhood. I think the problem is, more simply, that the mothers are kept on the sidelines or out of the picture. One could go so far as to see the Island itself as a "mother earth" figure, whose spiritual ailment (the plague) reflects her separation from her children.
Young Ben Linus' vision of his dead mother in the jungle has always kind of intrigued me, because it's not clear which "power" sent that vision. Jacob, as I've said, doesn't seem to shape-shift, and the vision seems a little too heartfelt, too "intimate," to be Smokey. So I'll hazard a guess that there is a "maternal" power on the Island which can also send visions, and that was her. Perhaps she was also the source of some of the other visions, particularly the ones that are animals rather than people (see: Kate's horse). And in the Christian paradigm, Mary mother of God is often thought to be nearly as crucial a figure as the deity. She represents compassion, and also purity, because she was conceived without "original sin."
One could take these themes in a lot of directions, and even if the preceding insights are valid, they don't dictate that the story must go in one direction. But I'll forge ahead and suggest that some reconciliation between motherhood and fatherhood--the notion of a FAMILY--will play an important role in the end, right up there with sacrifice and redemption. If I have to choose symbols that prefigure this solution, I point to Rose and Bernard, and Desmond and Penny, and Sun and Jin, and Adam and Eve in the cave. Dark and light, yin and yang, Lost sets up so many dualities, and many people have speculated that neither side will prove to "win"--both are essential elements. So, I'm suggesting, father and mother will prove to be key elements to make humanity whole, and resolve those "daddy" issues.
One further point: I also think there is a separate suggestion that the "daddy" issues will be resolved by the "children" growing up, and learning to stop living and dying by their father's approval. I think Jacob recognizes this, and his "hands off" philosophy is largely motivated by his belief that people need to make their own decisions (and his faith that they will come to the right conclusion, as he demonstrated by showing Jack the lighthouse and then hanging back). The rather gruesome "patricide" theme can, I think, be viewed more metaphorically: children must "kill" their fathers to grow up. But, the literal patricides (by, say, Ben, Kate, Locke (indirectly)) are too extreme, and hopefully the same outcome can be achieved by more benign means.
It has always struck me, and seemed important, that Christian was never more proud of Jack than when Jack turned him in for drunk surgery. Fathers like Jacob and Christian know their sons need to grow up and stand on their own. But perhaps Jacob and Christian both have been a little too callous in how they've gone about the process. And that is another area where a "mother figure" can perhaps supply the missing piece.