Was he evil? Just following orders? Following his own agenda or someone else's? I have no idea!

Good question, I think he's like a gun. It depends on who's holding it. I do wonder how he knew so much about things, like the existence of more ships.

Honestly, why would our creators go to such lengths to make it look like Darwinian evolution really happened?

I assumed they just started the process and let us evolve, of course that would make the Engineers a few billion years old.

Also, is there a less believable recovery from trauma in the history of cinema? "A machine just sliced me open, pulled out an enormous squid fetus, and stapled my midsection back together, but I'm good to go, really."
No, not in the entire history of film.

Charlize Theron's character could be edited out of this movie without making a single bit of difference. A one-note bore.
Yeah, was the "Father" line supposed to be a surprise?

I'm also pretty pissed about how much the trailers gave away. I think there should be a federal law, trailers are not allowed to show ANY footage from the last 30min of a movie.

Why would the aliens have seeded Earth with a map to their bioweapons lab?

1. By studying Earth language evolution you can apparently determine, vocally, the single source language. Linguists would be amazed to learn this.

2. When telling Charlize Theron how long she'd been asleep David reported it as X years, Y months, 36 hours, Z minutes.

3. If they'd already found 8 artifacts from 8 distinct cultures, why was it finding a ninth in Scotland that triggered the trip?

4. The use of artificial gravity and interstellar travel being completely unnoteworthy in just 80 years from now is a bit hard to swallow, with zero development in cold weather outerwear.

5. The star charts in the ancient ruins all pointed to a "galactic system" which is apparently a star cluster. A star cluster that couldn't possibly have been seen by acient civilizations from Earth. But the intro graphic tells us they were 3x10^14 km from Earth. That is only about 30 light years. Those would have to be pretty faint stars. Also, Earth based astronomy has apparently improved so much that we can tell that one of those stars has a ringed gas giant and around that gas giant is a single moon and it can support life.

6. Conservation of mass and energy in reproduction of life.

7. Language doesn't really work the way it is shown. You can't really trace back the languages to find a common ancestor of them all and be able to speak it.

8. They arrived at the planet, woke up, and set down all within a day. They apparently didn't do any mapping from orbit (since they were surprised by the giant mountain) and then lucked out to come down right at the military station. This is about as likely as picking a globe of earth and randomly putting your finger on NORAD.

9. They were all really crappy scientists.

Etc.

This one didn't bother me. As they were coming down it was shown that there were at least a half dozen of the domes in a line through that valley. Presumably there were at least a half dozen facilities and once it is revealed that a space ship lies under one of them it would be logical that a spaceship lies under all of them.

Plus, if David had spend enough time playing with systems that he was confident he could fly a ship solo then it isn't any stretch to imagine he'd learned a fair amount about the facilities they were in.

Yeah, I got nothin'. Ain't seen the movie.

To give one character's example: why did the geologist with the magic mapping orbs get lost if he's the one with the map? And why, if they were spooked by the mural room enough to leave did they decide to sleep there when they were trapped in the structure? And why, if they were creeped out enough to go in the opposite direction of the potential life reading, did they not run when the alien vagina snake appear out of the black ooze?

After creating a relatively simple gestation cycle for the Alien in the first movie (egg -> face hugger -> implantation -> chestburster -> xenomorph), why did the introduction of alien biology become so convoluted in this one? As far as I can tell, the vagina snake kills one guy outright - the black oil turns another one into a very limber big-headed killing machine - the introduction of the oil (or is it a drop of something else from inside the container) makes a scientist break down but first makes him shoot alien sperm (and is this different liquid that the engineer drinks in the opening shots which seeds earth?) - and then the alien-infected sperm automatically implants into the barren womb of a female human to turn into a creature that skips the egg stage to become an instant giant squid-like face hugger that will then skip the chestburster stage when implanted into an Engineer to become a xenomorph. Why make is complicated? Unlike Alien and Aliens, where the lifecycle is used to create a greater and greater threat as the movie progresses, this one seems to fall into the horror trope of "throw the biggest shock at the audience at any given moment."

I might not have a problem with a biologist who was completely creeped out by the overall situation but is then overcome by his professional curiosity when actually presented with an alien life.

I'm willing to cut some slack there. I viewed the black ooze not as something with a pre-set biological path but rather as a reproductive pragmatist, a proto-ooze that warps its host in some way towards reproduction but not necessarily the same way everytime.

The "Alien" at the end may now have a fixed, simple reproductive path but the black ooze need not yet. And exhibit differently in each host.

But I'd hope some further explanation ended up on the cutting room floor. And I'm sure I'm just fanwanking what was really just a desire to do more horror tropes.

1. If the BBAs in that facility were destroyed by the goo, what contained it again for the arrival of the humans?

2. If the intent was to deliver the goo to earth for some purpose, and the BBAs managed to contain it with just one survivor, why did he go into cryosleep instead of continuing on the mission (which was apparently his first thought on being awoken. It isn't like he killed the humans and went back to bed.

3. Why did the BBAs have such ****ty hologram technology? And isn't video recording all the activity in the faciity but then having it play back in the actual geography of the recording kind of pointless? Maybe some BBA Space Detective would like to know what happened with the 3 BBAs running down the hallway, resulting in a decapitation without actually having to run down the hallway with them.

4. The Death of Charlize Theron was a bad Warner Bros. cartoon. In cartoons, whenever a tree is going to fall on someone the character tries to outrun the length of the tree (say 100 feet) instead of just moving 15 feet perpendicular. Charlize Theron is as dumb as Wile E. Coyote (and Rapace only slightly less so).

5. Why in the world would they invent a self-service surgery machine and then "optimize" it only for women. Is memory storage really so hard to find in the space faring future? Maybe if David had been forced to leave his Blu Ray of Lawrence of Arabia at home. And then after that it didn't seem fazed by the presence of decidedly not male organs.

Why go to the great lengths to precisely set up the exact photo-perfect situation encountered in the original Alien - only to depart from that a few minutes later, and hence make that very careful set up never having happened ... so that the situation encountered in Alien was ... what? Yet another of the buried spaceships that happened to have yet another lone surviving Engineer who was also awakened somehow??? This was a too-cute set-up turned into a giant WTF? for me.

I can buy the Engineer being anti-human, but the murderous rage of killing spree was ridiculous ... and saving the Earth is one sci-fi cliche that I cannot stand anymore

If we assume the planet is indeed a weapons research facility, then earth becomes a source for lab rats, which is why we have their DNA.

As for the BBA, If I was a lab worker and woke up to find a bunch of test rats running lose (especially ones who might be carrying the space equivalent of Ebola) I'd kill them first and ask questions later.

You could also view the "star map" as an intelligence test. Ooops, the rats figured out the map. They have gotten smart enough to escape their cage (aka earth). Time to kill this batch off.

The Engineers were stockpiling the weaponized version of the black slime so I don't think anyone/thing had to repackage it after it got loose it was already there. Obviously a little goes a long way.