Prometheus Problems - Where Did The Plot Go?

I finally saw Prometheus the other day and was disappointed.  I didn't go in with high expectations after hearing all of the comments and reviews about it from all over, but I was still hoping I would enjoy it.  I thought it was an A class movie for fantastic visuals and special effects trapped in a B or C class plot.  The movie had lots of neat stuff and cool moments, but I kept falling through the plot holes that detracted from the enjoyment.  It was one of those movies that would have been improved if you could have sympathized with any of the characters too, which I could not.

Also, if you like the movie - power to you - as I know lots of people who liked it.  I'm just giving it a C for an average grade.  I do agree with the critics that the android is awesomely acted though!

Hicks Action Figure vs Alien Queen.   Thorsten Becker / Flickr

WARNING : Spoilers ahead as I'm going to talk about the holes in the movie that detracted from the enjoyment. If you keep reading and want to see the movie - stop! Don't read on!

1. It starts with a very powerful and wealthy man who hires a bunch of misfits for a trillion dollar expedition to seek immortality. This is the best crew unlimited money can buy?!?  You gotta be kidding.  They all have emotional baggage a mile long.  Psychological profiling has definitely not improved in the future - or these were the only people desperate enough to go.  The crew for Aliens vs. Predator - the first movie was better.
2. Never trust the android, or any AI named HAL or ALICE.  HAL from 2001, ALICE from Resident Evil and King of Thorn.  Might not want to name your daughter Alice either :)
3. The geologist on the expedition was smart! He wanted to bug out when they found actual dead aliens in a labyrinth in the pyramid.  He says dead aliens aren't in my contract and leaves with a pal (a biologist with no common sense - apparently plays with upset cobras for fun in his spare time). 
   Somehow this guy - a geologist who is an outdoorsy type - who should have a good sense of direction and understands mapping gets lost on the way out when he is under no time pressure.  However, everyone else who has to suddenly evacuate later manages not to get lost in a hurried panic to exit (not to mention they don't see the geologist on the way out). One review I read said that the movie seemed to be missing pieces or it was like 2 plots jammed into one film and I have to agree.  This could be explained by something on the cutting room floor.
4. The above evacuation due to a mega storm rushing down on them was also kind of dumb.  You're telling me that this multi-billion dollar spaceship doesn't have weather radar that could spot this storm a couple of hundred miles out or even as they came down from space?
5. The automatic doctor and surgical unit is only programmed for men?  This scene later on was kind of stupid.  You're telling me you only have enough memory for one sex with nanotech and holographic storage? It was especially bad as the auto doc was in the Weyland Corporation's FEMALE representative's life boat module.  This is the woman who hates risks and takes everything into account.
6. When are they going to bring good guns on these expeditions?  It isn't Alien where they're not armed as they are a mining vessel.  This is an outfitted expedition that should have state of the art weaponry, not wispy little shotgun type weapons (probably some wispy .410 bore shotgun to boot).  Some assault rifles with AP rounds or FULL AUTO shotguns with flechettes and multi-shot grenade launchers please.  Enough of the Starship Troopers movies about popguns vs alien monsters on a mass scale.
7. The captain doesn't know that there is a secret section on his ship with a secret passenger plus entourage that apparently anyone can walk into. I think this is another one of the two plots jammed in one movie items that I talked about earlier.
8. There is apparently no night shift on the ship to watch the bridge.  A common theme with the Aliens movie (BTW Aliens is one of my top 10 SF movies) where you leave your powerful vessel in orbit with no crew and no way to drop nukes from orbit to back up your ground team.
9. Wasn't the heroine supposed to be sedated?  Her escape scene and surgery was pretty cool otherwise, but anti-climactic as no one even bothered to chase her. 
10. The stuff about the Promethians and the origin of humanity.  There's an evolutionary problem with this idea, but I'm going go along for now as this idea has popped up numerous times in SF including Star Trek and 2001 a Space Odyssey.

Overall, I did kind of enjoy the movie. Ridley Scott is an a great director.  I just wonder what happened to the movie's plot.