Apologies if this theory has been submitted before. Okay here's my theory on why the Island was udnerwater and why Desmond was on the plane in the alternative reality (or at least, why he wasn't on the Island).
The Losties detonating the Hydrogen bomb WAS The Incident all along that the Dharma folk referenced in the videos, it just never caused what Daniel thought it would i.e. it didn't make it that the Hatch was never built. It caused them to need to build the Hatch and push the button because the Hydrogen bomb caused it to and to let out the energy unless it was supressed (by entering the numbers).
So the alternative reality where 815 never crashed wasn't caused by them detonating the Hydrogen bomb but rather it's just what WOULD have happened had they not crashed on the Island. The reason The Island was under water was because of the Losties not being there to detonate the bomb, meaning whatever the Dharma folk did at the Swan work site (hitting the energy pocket) that was the thing that caused the Island to sink (remember, it had to be AFTER the '70s when Dharma was there because you saw the Barracks, Shark, with Dharma logo etc), some sort of magnetism pulled/pushed it under the water.
With regards to Desmond being on the plane, this theory does go a ways to explaining that (or at least why he wasn't on the Island pushing the button): If the Island sank in 1977 (remember it HAD to be after Dharma was there because we see the Barracks with the swing set in the underwater shot) when the Dharma folk hit the energy pocket then that would presumably kill everyone who was on it, including Widmore. Which means he would never father Penny, which in turns means Desmond would have no reason to go on that round the world race. He just happened to be on flight 815 (or perhaps the Universe was trying to course correct, as Eloise Hawking said it has a way of doing).
It makes more sense than the Losties causing the alternative reality because, as I said, they wouldn't have been to the Island in the first place to cause the detonation of the hydrogen bomb.