"and throws middle school level puzzles at him, knowing he only has a 4th grade education."
That made me laugh :)
And, generally speaking, I think everyone is trying to give much too complicated interpretations for a simple game. This game is simple in it's every aspect: simple graphics, simple art design, simple coloring, simple sound design, and I'd say simple story too. Also it doesn't use words during the game (save for "Hotel"), so I'd say that the developers pretty much tried to reach for something compelling and deep but unusually simple. Thus, I'd try to understand the story as simply and directly as possible, without far-fetchet interpretations or speculation, just taking straight from what the game tells us (and from the description in xbox live arcade: "Uncertain of his sister's fate, a boy enters LIMBO"). Please note that if I call anyone's theory far-fetched it's not that I'm being... ugh, forgot the word... trying to invalidate what others say just because I say they're wrong, your theory is just as valid as mine, it's just that I'm trying to see the story from a simple perspective, to fit with a simple game, as I said.
Anyway, onto my interpretation... The car theory at first seemed to fit with the ending of gravity shifting puzzles to me at first, but really, I think it's way too far-fetched to think that that thing on top of the tree at the main menu screen is a car, the developers really wouldn't have made it like that, plus it's atop a tree, that has a ladder on it's side, so I think it's just a tree house taken down by time. I agree with almost everything that Maze_ wrote, but I do think that the developers tried to add a little more depth into the game, because the main menu screen is clearly the same as the ending place, but torn apart from time (Implying a concrete storyline, and not so much as just a journey through an atmospheric game to find the sister). First of all, I do think the boy is indeed a boy, and always was, because probably most of us knew a definition of limbo as the place where kids go if they die, and I think it's the most popular definition for it, so I'd say that the protagonist died as a child, being uncertain of his sister's fate, and passed onto limbo. We do not know if he did it on purpose or not, but I think not, because really, a kid comitting suicide at that age? Also they only say that he was uncertain of his sister's fate, but she might as well be alive for all we know, maybe she was lost, and the boy didn't know what happened to her, but when he died and woke in Limbo, she was the first persone that he thought about, and he set onto find her (though she might not be dead, and not in Limbo). Now, because I believe that developers did intend meaning for some things that were obvious enough, I do think that the eyes carry some meaning, and it's the "being alive" (also seeing as the eyes are popularly known as "the windows to the soul" or something like that), and he, all along the game, is the only one that has eyes, thus I think that he is only living thing (with a soul) in limbo (or at least the part that we see of it) and all the other creatures and persons are just created by limbo as hazards that are inherent to that place... and his sister appears with no eyes (and I believe too far-fetched to think that she was just looking in the oposite direction, this game is all about simplicity and I think developers meant something with that, also, the boy always faces the screen despite whatever he does, so clearly they meant this as a sign), I believe that his sister is just another one of the tricks of limbo, and that when he finds her, he is fooled by it and stays with her as if it where his siter. As soon as I finished the game, and saw through the credits, that screen appeared, and, since the image appears, and a short while later the menu appears, I thought it was the epilogue to the game, and it struck me that, after finding his sister, the boy died along with her. When the menu appeared, I realized it was not the epilogue, but the impression stuck with me, that after finding his sister, they both just stayed there, with nowhere else to go, and died there. I do not think that that image is before the events of the game because the developers clearly wanted to set the "limbo mood" through the black and white visuals, and so I think that throughout the game we do not see a single moment that happens outside limbo. Therefore, I think that after being fooled by this vision of his sister (I believe it's that because it has no eyes), he stays there to die... maybe at peace because he found his sister, I do not know.
And that is all that I have figured from the game thus far, I think that the places he goes through are just the hazard filled locations of Limbo, though the Hotel does seem to stand out, I don't know what it means, and I don't think that the game is a metaphor for his life. It's just Limbo. I also don't know what the eggs might mean, though I do think they meant something with them.