Why? Well, I figure that when the show started, tptb didn't know how long they had to tell their story. Maybe they'd only get one season. So it stands to reason that they'd put enough information into the show's beginning that they could have, somehow, cobbled together some kind of ending. Yes, it would probably have been rushed and unsatisfactory and we'd have missed out on Alpert, Ben and Desmond, Juliet, Miles and Daniel... and that's a whole lot to miss! But anyway, S1 has to have some serious goods in it. Which is why I went back and read up on the eps (watching them all will have to wait a while) to refresh my memory as to what came first.
Smokey the "monster" (or whatever it may turn out to be) was introduced right from the start in The Pilot. We saw it chase Kate and Charlie and Jack, we saw it kill 815's pilot and generally make noise and misbehave. Since then we've seen a lot more of it, but I'm guessing it will be S6 before we get any big answers here.
The Black Rock
How did the ship get to be way up on an island mountain side? What happened to the people on it? This also ties in with how Yemi's plane could have reached the island. Do Alpert and/or Richard have a connection to The Black Rock? Does Widmore?
These seem to have gotten their explanation once we saw that the Others had cages for polar bears. But I'm not convinced that totally explains it. Charlotte found a several thousand year old polar bear skeleton in the Tunisian desert wearing a collar with a Dharma symbol. How did that happen? Turning the donkey wheel bumped Ben into the future, not the past. And how did the bears get there anyway? Maybe the island was in a polar region at some point?
Walt is special, that much the show seems to have confirmed early on, but we've never really gotten an explanation as to what he's capable of doing. The Others interest in him was not just because they can't procreate and therefore would need children, as was shown in the mobisodes, they were doing something to him and what he did in turn freaked them out. We've seen birds fly into windows a lot when Walt is upset. And later there's his whole turning-up-soaking-wet-and-talking-backwards-to-people schtick. And even more recently turning up all grown up to tell Locke to get a move on. Clearly, Walt can appear in places where he is not physically present. Clearly he can affect his environment somehow. Hopefully he'll be back in the cast for next season so we can find out what the heck is really going on there.
After seeing the mobisode "So It Begins", I'm convinced that Vincent may actually feature a lot more in the last two seasons of the show. If he was "communicating" with Christian every time Walt and Michael were looking for him, then what were they communicating about? I want a Vincent flashback ep that shows us everything he's been up to when he was off in the jungle!
Dead man walking
Very early on we saw that dead people can be seen by the living on the island. Christian showed himself to Jack in "White Rabbit", seemingly to guide him to water and the caves. Just like we later saw with Yemi, his body disappears but he sure doesn't. Is he a manifestation of Smokey? A zombie? The island somehow projecting itself? The theme of dead people being able to interact with the living and communicating with them seems to run throughout the show and the addition of Miles to the mix this past season makes me think we might finally start to find out what that's all about.
Adam and Eve
Jack and Kate find the two skeletons at the caves. On the bodies is a pouch with one white and one black stone. According to tptb, once we find out who Adam and Eve are, we'll know that they knew where the story was going right from the start. Some people say that Adam and Eve will turn out to be Desmond and Penny. However, I find it more likely that they are two people we knew from S1. Jack and Kate? My own favourites are Rose and Bernard.
The island heals Rose's cancer and fixes Locke's legs. The island's "energy" may be responsible in some fashion, but then how come Ben gets a tumor and Jack gets appendicitis? Because the island is "displeased" with them? Just like when it won't let them die, but, you know, the opposite? Is it the island actually, actively healing them (as in: it's acting like a person), or is it more that it's properties and fate and destiny and time somehow make these things happen "naturally"? Ben tells Juliet that Jacob cured her sister's cancer. Is Jacob somehow able of making people sick and healthy? Is he the island? Ugh. Just another one of the mysteries that seems like you have part of it figured out but when you think about it some more, you really don't know anything...
I already wrote about them. Some of them may be the Hostiles/Others communicating but a lot of them have to be something more. Dead people still able to make themselves heard? That's what I'm starting to think after S4 and seeing Miles in action.
What the heck was the vaccine all about? Ethan was injecting Claire with something. Much later we saw Claire get sick and bleed, and this was somehow triggered on Ben's orders. So was it a vaccine or just part of that ruse? Charlie worked really hard to get Aaron and Claire vaccine in one episode and we know Desmond used it too... We've never gotten a satisfactory explanation about the vaccine and what it actually was supposed to do.
Claire's psychic told her that her child should not be raised by another/an other. Then said she should give the baby up for adoption in America, basically putting her on flight 815. And in "Raised By Another", Claire has a very weird and possibly prophetic dream about Aaron:
Claire wakes up in the night. A baby's cry is heard. Claire sits up with a confused and concerned expression on her face; she looks down and feels her stomach, noticing that she is not pregnant. She hears a baby cry again and starts off into the jungle in a daze, apparently looking for the source of the crying. Claire sees a light in the jungle and walks toward it, where she encounters Locke sitting at the table at which she received her psychic reading (in her flashback later in this episode); the psychic's electric lamp is also present. As she approaches, Locke is drawing what appear to be the psychic's cards from a deck one by one as he stares down at the table (the first one making the sound of a metal against metal, like a knife being unsheathed); they exchange a few brief words:Yep. Something is up with Aaron. Not sure what yet. I guess he has to go back to the island in S5, but I really wonder how they'll make that happen. I just don't see Kate taking a little kid back there.
CLAIRE: What's happening?
LOCKE: You know what's happening.
CLAIRE: But I don't understand. Why --?
LOCKE: He was your responsibility but you gave him away, Claire. Everyone pays the price now.
As Locke finishes saying this, he looks up at her with a creepy expression on his face and has one black eye and one white eye.
I don't think these will ever be totally explained. The possibly canon explanation of The Valenzetti Equation is probably as much as we'll ever get.
My conclusion is that we really don't know a hell of a lot more about the island than we did in S1. Yes, we know more about what's been going on there, but no real answers about what it really is and why it's so special. Lots of hints (Daniel talking about light refracting oddly, donkey wheels, Dharma, hatches) but nothing concrete that actually explains what it is and how it does what it does. I guess this is because the actual nature of the island is the key to all of Lost, and we won't find out until the very end. Hopefully we will find out then at least!
All screencaps thanks to Lostpedia.