I think there are two issues:
First one is that many people wanted Prometheus to be more Alien-like. I agree with the comments above, with regards to why, in that case, Lindelof's script was what they went with.
Second issue is the quality of Lindelof's script (accepting that the thrust of it was 'less Alien'). As other's have said before, Lindelof is awesome at the 'broad strokes' (thank's David!), and overall, that to me made Prometheus a good film. However, the detail is the killer, and to me, that's where the most of the problems that get talked about on this forum come from. Inconsistencies, continuation issues, elaborate set ups for weak payoffs, seemingly important situations (and obvious nods to Alien) that turn out to never be explained, or even suggest they can't be given the context they appear.
Prometheus (in Lindelof's hands) essentially became a bit like 'LOST!' in space. Lots of 'OMG' set ups with limp payoffs. It's like he expends all his creative energy coming up with a shapeshifting, biomechanical, 8 foot, polar bear looking hybrid man in black, which we are teased with to the point we almost burst. Then, when we get the big reveal, we never find out who/what it is, just that whatever it was has just come back from the grocery store with two lettuces and a carton of milk! WTF! I mean, I know I'm exaggerating, but really, that's what it's like. 'Look at these Engineers run in to this room - something must be chasing them, and that room will keep them safe'. 'Now look at this pile of Engineers, not in that special room, but all burst open and scary looking'. 'Now let's forget them, and look at the ship'. 'Now let's look at the pyramid.....ship.....pyramid.....ship....pyramid....now, forgot those other Engineers, they won't be worth investigating further - oh, look, a flute that starts a Juggernaut'
