Spaihts wrote an Alien prequel script, complete with facehuggers, eggs, chestbursters, and drones.
Sometime after his completed draft but prior to shooting the decision was made to back off from the "Alien-ness" and make the film a prequel that doesn't actually lean on the prior films. So Lindelof was brought in to rewrite large portions of the script and remove the blatant Alien stuff creating new monsters instead.
I think many complaints are based on the fact that the film should've been over 2.5 hrs but was cut down to 2, and that like The Abyss the story will be clearer once that stuff is back in. The rest is likely Lindelof's doing as being involved with Lost for so many years you know he's good at obfuscation and confusion.
As for sequels, no decisions have been made yet as to if they even will make one (although it's a good bet one will be attempted at least as far as the script stage).
The Jedi Master
The anteater is wearing the bagel because he's a reindeer princess. -- my 4 yr old daughter