[mousepod]

Alex, I think you touched on many of the logical plot issues.

There were others, of course, which mostly had to do with the behavior of certain characters.

Spoiler:

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?

And as for the internal logic...

Spoiler:

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'm sure there's more, but I'm at work now and apparently I have work to do...