I haven't had a chance to read any recaps yet, but a couple of things are bouncing around in my head. Richard told Sun that he saw all of our Losties die back in the 70's. If that's true and whatever happened, happened, that would mean that Hurley, Jin, Miles, Kate, Jack, Sawyer, Juliette and Sayid never make it back to 2007 and the coming war. I'm having a hard time believing that LOST would do that to us. To me, something must be changed...
The logic of detonating Jughead is fuzzy to me, too. Did I hear Faraday say that the H-bomb and the electromagnetic field that Dharma was about to drill into would neutralize each other, or am I imagining that? If so, wouldn't they need to be closer together, or something?
Speaking of Jughead, Dharma's building the village over it and the Others eventually moving into that village would certainly explain fertility problems....
My guess (and I'm spoiler-free so don't tell me if you know I'm right or wrong; I'll find out soon enough) is that we have one time flash left this season, and it will reunite our groups of Losties in time (in contrast to all the other seasons, where we've ended with the Losties being split up). The time flash will coincide (or be caused by) the Incident, so Richard will watch the Losties disappear in a flash of light and conclude that they were vaporized in the Incident. I think that Jack's group will move the bomb through the tunnels to the Swan site, where it will somehow interact with the magnetic anomaly there. Some version of the Purple Sky event will ensue, Losties will time flash, and Richard will conclude that they were vaporized (he'd seen Locke time flash in 1954, but he didn't see the light that the flashee's experience).
My guess is that the Incident will also cause the fertility problems, as living above a bomb has had no effect on them so far. (Though it could have had an effect on their children - radiation on developing reproductive organs can have an effect - but this wouldn't explain the effect on people recently arrived on the Island.) The fertility problems seem to be somehow time-related, so I think the Incident somehow skews time somehow.