I really hope for an extended cut. It needs it just as much as Blade Runner or Kingdom of Heaven did. Usually I'm not into films spiraling towards 3 hours but this film can hold interest through intrigue and could easily hold you for another 30 minutes. But I think somewhere along the way someone forget that a certain amount of exposition would have just made sense of some of the character assumptions. I'm sure there is missing character stuff and I'd be very surprised if there wasn't more than just a frown of dissatisfaction from David when Shaw appears post op, there must be some fallout from her attacking Ford etc.
Also, if there are 17 crew members I reckon I can only account for 11 deaths, so either that's a fairly random number or some major battle with Fifileld was seriously cut down - given Janek's cut line "Kill everything" perhaps Fifield was spreading the infection wildly amongst his attackers making it neccesary to sterilise the landing bay. ?
It could certainly do with a bit more gore (which is something else I never thought I'd say).
I like the film, a lot, but there's no doubting that flaws could be ironed out if the appropriate extra footage exists.