Honestly, you can take enthusiasm for a movie only so far.
Don't take this as one who wants to argue each point, because if you did not like, you did not like it. But I am curious, so I responded with some of my thoughts to each point. I had zero expectations when I went to see the film by the way. I learned not to expect anything after the let down of Return of the Jedi when I was a child.
The first big moment of panic I had that the writer might not be particularly smart was when Shaw announces to the audience upon entering Vickers quarters "wow! A Super duper limited edition and very expensive automated med-pod!" - Scott may as well have just put a captioned arrow on the screen that points to it and says PAY ATTENTION! - THIS WILL COME IN USEFUL LATER ON IN THE MOVIE! (and this is way before we see Shaw, an archeologist, appear to be very capable of operating said incredibly exclusive and very hi-tech medical equipment)
Agreed, that was blatantly telegraphing something to come, but I had also seen the alien removal scene in the trailer, and saw the med-pod on the website, so I already knew it was coming, as did just about anyone who saw the trailers. Did not bother me enough to dis the film. Just made me PO'd that too much was shown in the trailer.
I guess though you could argue David had 'secret motivations' for taking it and here's the thing that chaffes with David - you can make absolutely anything fly in this story because David's an android: given what little we know he's wildly open to interpretation to the point of being a blank page.
His motivation for taking it seemed simply to be cruel to her, and it seemed obvious in the scene when he took it. His attitude towards her seemed to change after seeing how far she was willing to go to survive. As far as him being a blank page, he seemed the most readable and understandable character in the whole film to me.
But what about those reactions to Shaw collapsing after the C-section? Right, ostensibly there were none.
Actually, someone got her a robe and helped her sit down, but that was one of the few issues I had with Prometheus. I thought it was an odd scene, but the first thing in my mind was not "bad writing", but, what the hell is going on in this surreal scene? The fact that David was so completely focused on Weyland in his presence that nothing else mattered to him other than prepping him to meet his maker, was very telling. That was all that was important to Weyland at the point he found out one of the Engineers was still alive, so that was all that was important to David. The crew were essentially expendable before the ship even left Earth.
Even David who has a clearer idea than anyone might want to show more of an interest than a trite quip - I mean, it was his experiment
His experiment? Infecting Holloway was. I don't think David had a clue she would be infected, let alone impreganted by Holloway. How could he have anticipated or planned that? THAT would have been bad writing. Once he found out she was pregnant, I got the impression he was completely done with her. Freeze her and we will study this thing later. He already knew he was taking Weyland to the engineer at that point. A lot happened from the time she blacked out until she came to in the med lab.
Really - you will not find these kind of wtf clunkers in Alien or Blade Runner
Despite my love of Alien and Blade Runner...oh lets not even go there. Despite the fact that these are now considered untouchable classics, there are clunkers a plenty in both films...especially Blade Runner. I well remember those discussions with my fellow sci-fi fanatics.
Why isn't finding more of the 'Engineer's running' hologram explored? Why are they only conveniently shown a tantalizing snippet?
When would they have had this opportunity? The first visit was very brief, and things went to hell immediately as soon as they got there on the second, prompting them to leave immediately.
Why isn't the pups hologram scrutinized for clues re: Fifield and Milburns accident? Don't they record it? Does anyone actually ever really use it anyway?
Curious. That makes me wonder what you were paying attention to. Charlize can be a bit distracting

The hologram was in use and being watched constantly from the moment the pups were released. The captain and at least one, possibly two other crew members in the background on the bridge, were monitoring it throughout the night while Fifield and Milburn waited out the storm, including seeing the life form appear off and on. He knew exactly where they were when they lost contact and told Shaw when they were suiting up for the return after the storm. Not to mention numerous scenes of he and Vickers studying the hologram throughout the first scout scene.
As a side note, people have complained 'how could Fifield map the caves and then got lost?' Actually Fifield was the geologist. He carried the pups, which mapped the caves and sent the data back to Prometheus. There was nothing to indicate Fifield had any type of portable hologram device with him. All he had to do was ask Prometheus where they were and where to go if needed. Presumably, in a normal job, his forman would have told him where to do his work after the mapping was complete. The one line he said as they were leaving the was something like "we came here before". This was within minutes of the ship calling and telling them the storm was coming, so I did not equate that to being 'lost', just one wrong turn. They talked to Prometheus literally 10 seconds later. But, the man was an incompetent idiot, and was written that way for a reason. He was nothing more than a union labor Weyland company man. And this was just another routine geology job to him, until it became apparent it was not.
Why would the Captain presume it was a glitch and not a life form the pup detected and at least get others opinion - they have travelled x billion miles and actually found an ET installation after all, quite possibly the most significant find. Ever. At least entertain the idea the pup was working to spec.
Someone already replied to this above, but the captain did tell Fifield and Milburn there was a lifeform. Then the signal was only intermittent, indicating a possible glitch. Not much else he could do from the Prometheus bridge during storm other than tell the team about it after the storm passed. David went directly to check that pup out when he returned after the storm, by the way. It was the first thing he did.
Why would the Engineer who previously prioritised his mission to Earth above getting Shaw...
He actually let Shaw walk out of the pilot room after killing everyone. He never made a move to get her. It came across that he simply let her go. Out of pity (she was just wacked in the gut by Welands man, who the Engineer killed), or simply that he saw her as no threat.
...now prioritise getting Shaw above grabbing another ship and getting on with his obviously pressing engagement.
He calmly went to work powering up the ship after letting Shaw go, setting the navigation, or whatever he was doing. Even that did not seem to be a pressing engagement from what I saw. It was not until after the humans caused his ship to crash that he went to get Shaw. He had just seen evidence that these humans were willing to sacrifice their lives to stop him. Was he going to prevent her from doing anything else since, as the only human left alive, she had access to the other bases and ships? It may have been as basic as wanting to kill her out of anger. He did not simply swat her into a wall and crush her when he found her though. She had an axe in her hand and he pinned her to a wall, I presumed to disarm her. What is more interesting to me is was he going to kill her, or take her with him, and what did David say to him that whole time, and how did David know he was going to her. I know, I know, you probably see all that as 'bad writing' as well
Making out it's a more finely crafted and intelligent movie than it is though just lowers the bar.
For whom? Not for those of us who see that it is a finely crafted intelligent film. It is not perfect, but I have yet to see a perfect Ridley Scott film. This ranks among his best, and compared to about a dozen other top sci-fi films from the last 20 years or so, this makes my list.
But we all have our individual tastes, which makes these discussions interesting.