I've been doing some brainstorming lately trying to figure out how all (or at least most) of these loose ends we still have in the show may be brought together. I personally don't think they'll all be answered as the show is more about the characters and the journey and choices they make, but it would be nice to have some closure on some of the bigger issues in my opinion.
One of the things we know, is that the US Army had a camp on The Island as early as '54 (if not earlier due to them having been apparently wiped out by the Others by then), but...how did they become aware of it? I had an idea that ties up another loose end as well, and I'm wondering how close I am.
We know the building of the Swan created an "Incident" (more on that later) which was an immense release of electromagnetic energy stemming from "the Island's unique properties" due to DHARMA drilling into it. We have seen the same sort of "incident" (to a degree) when Ben turned the FDW (and later/earlier, Locke)and when Desmond used the Fail Safe.
The Fail Safe is what allowed Penny (and possibly Widmore) to "see" the Island, and causing Penny's "team" to wonder if it was a false alarm since they had missed a previous one (presumably the "almost" incident when 815 crashed).
Ben turning the FDW caused the Island to move (not only through time, but apparently through space as well since it disappeared from it's location), but the effect, both sounded and looked (until the Island disappeared) seemed to be the same.
Now, we don't quite know when Locke was when he turned the wheel to get the Island to stop skipping, and although I'd like to think it was '77 (or 2007, either of which would tie up loose ends nicely in what happened to Ajira 316), I don't see '77 being viable. DHARMA was just becoming aware of the FDW at that time, and I'd think the fact that it was off it's axis causing the Island to blip through time would be noticed by them.
We also don't know of any repercussions (yet) of The Incident at the Swan station, other than that the protocol was adopted by DHARMA to press the button every 108 minutes.
All of these (including the FDW turning, and yes I'm assuming here) represent a release of the energy inside the Island. We've also been told (as was Annie's class) that the volcano on the Island had erupted in the past. Perhaps it was this eruption (and subsequent release of energy) that drew the Army's attention in the first place? Or was the Army just lucky enough to have picked that Island for their testing? The pictures and dates in The Lampost station would seem to say otherwise.
Now, this is where things get weird, (and in this show, that's really saying something).
I've always been a Whatever Happened, Happened person, and while I still am, I feel a more correct term is "Whatever Happens Is What Happened". Eloise told Desmond about course correction, and I look at it like this. There's a river, water flowing down a mountain and headed towards the ocean. You take a large rock and throw it in. Was the rock there previously? No. But has it changed where the river ends up? Not at all. Certain things can be varied, but eventually...somehow...things end how they should, even if it wasn't how they got there the "first time". Another way to look at it caught my attention in the Dr. Who special "Water on Mars". He stated that certain things in the timestream "were fixed points, and must always happen". This would seem to fit with some LOST mythology in where certain things can be changed without changing the bigger picture as long as the things that *have* to happen always do.
Just my two cents.