My thoughts on Season 6 so far:
The alternate timeline is real and running concurrently with the Island timeline. I think we must assume that the bomb worked and sunk the island in that version. Obviously from the differences between ep 1 and what we have seen this season, the butterfly effect has altered things there somewhat.
The problem is, for the bomb to work and sink the island, somebody had to detonate it, but if Jack etc never crashed on the island and therefore never went back to the seventies, they couldn't have detonated it. The creation of a parallel timeline resolves this... it seems that all the characters in the parallel universe will now come together in a different way (eg Locke getting a spinal consultation from Jack)... perhaps they will eventually end up on the island by different means because that was always their fate. They can then go back to the seventies and detonate the bomb, completing the cycle. However... the island is now at the bottom of the sea, so that can't happen...
I know this has all been said by others... just trying to sum it up for myself really.