There were a lot of words spilled on it in one of the Prometheus threads (I believe it's the one about
Jon Spaiht's original draft) but it comes down to this: Studio wanted the film to be less xenomorph-related. Ridley agreed. Studio wanted someone with more experience than Spaihts to be on the picture. Ridley agreed. Ridley grabbed Lindelof.
Ridley then, as he had done throughout the majority of pre-production (as seen in a LOT of the footage from the 3hr documentary on the making of) spent most of his time getting sloshed on wine and spewing shitty ideas into the ether. Lindelof then had to take those ideas and rewrite enough of Spaiht's script with them so as to secure the credit he'd been hired to provide.
All that aside - movies don't work like books in that the storytelling is largely dependent on the written word. More often than not the directors/actors are applying their own changes once its out of the writer's hands, and editing can even further change the storytelling intent. Prometheus isn't broken because Lindelof wrote a broken script. Prometheus is broken because Scott asked him to write that broken script to his specifications, signed off on it, and then directed an even MORE broken movie based off that skeleton.
Look at Orci/Kurtzman and the difference between Transformers and Star Trek. The scripts are, honestly, not too different in quality. Now give one to Michael Bay, and watch what happens. Give the other to JJ Abrams and Damon Lindelof. Vastly different result.
Side note: I'm wondering if the shot of the Enterprise coming up out of the water came from the writers looking to top the moment from Star Trek where the Enterprise rises through planetary rings. Because that was probably the single prettiest shot of the whole movie.