Get the writer of The Tree of Life. Or, better yet...get Jon Spaihts back.
At the end of the day....I blame Ridley Scott for the gaping holes left by way of editing. Lindelof's contribution.....I don't know. The problem with the film is more in the way it was put together, as opposed to the writing.
There are elements (a lost geologist, among many) that were poorly written.