Fanwanking is very different from using smart thinking to connect the dots.
Connecting the dots in Prometheus would be for example deducing that the Hammerpedes are mutated worms. The transformation is not shown happening, the audience is required to put two and two together. There are worms in the goo+the goo mutates organisms = the worms mutated. There is quite a bit of connecting the dots required in Prometheus, and that is a good thing.
Fanwanking is inventing explanations to try and ignore flaws and errors in continuity. That's what you're mainly doing.
And don't get me wrong, fanwanking can involve smart thinking, if it makes the movie better for you that's great, it just doesn't make it a de facto great movie, and your explanations may work for you but they're not actual facts that should be deduced by smart audiences. In fact, the more you have to fanwank when watching a movie, the less "great" and "smart" the movie is. And there's a LOT of fanwanking required to enjoy Prometheus, as you are proving.
Let's take that example :
Everybody on the ship knew what happened to Shaw. Ford & Shaw would have had a confrontation also, just like Lambert & Ripley. It was just not shown in the movie. The film-makers thought of not spoon-feeding inessential details and extend the runtime to bore the smart audience.
I don't even know where to start with that one. How is it inessential to witness the reunion of two people when one of them was almost responsible for the other's death following the orders of a robot, all the more when said reunion is so they can go on another mission together with the same robot?! Because it should take seconds if these two supposedly SMART people had a confrontation for them to figure out something is wrong with David. So if a confrontation did happen you'd think a smart movie would have taken on a different path following that, given that Weyland relies so much on David.
Ford seems like a nice person and has actually worked with Shaw ( Engineer's head scene ), I actually would have been very interested in seeing her realise the full horror of what Shaw went through and how she was a part of it ( all the more that the actress is really good, just saw her this week in The Witch, made me all the more disappointed at how underused she was in Prometheus ).
So what you are deeming "inessential" is for me something that makes a movie worth watching. Seeing characters interact and having to go through complicated, tough situations and emotions is a big part of the fun when watching a smart movie. The aftermath of Shaw's C-sec shouldn't have been one line by David "impressive survival skills". Not showing anybody being concerned by the movie's protagonist being almost naked, bloody and stapled isn't smart. We need these people to show realistic human emotions to relate to them and actually feel involved when they die.
See, in Alien I actually cared about Lambert, because of all the scenes she had, and all the confrontations she had with the crew. She was acting like a realistic fragile person crumbling under pressure. So I was really into the movie and sad for Lambert when she died. That is good film making. And yet Lambert's death scene still has a "connect the dots" element to it as the clues are there for a smart audience to deduce that the Alien raped her. Smart filmmaking is knowing what to show and what not to show. The truth is that some of Prometheus is just NOT smart.
For you a confrontation between Shaw and Ford was inessential, and yet the result of your inessential scene not being there is that when Ford died I really didn't care or give a f**k ( and neither did Shaw ). Ripley being concerned for Lambert was a nice touch in Alien... but then again Alien IS a great movie.