1. No, that was very clearly an engineer seeding life on earth, in a sacrificial rite. As I said, that scene made it clear how important, almost religious, the engineers take their responsibility, and explains why the engineer at the end decides he needs to wipe out the idiots who just woke him up.
2. No, it was very clearly not the first Alien. The facility on the planet had obviously manufactured xenomorphs before, as evidenced by the mural. The whole places was a bio-weapons facility, and the xenomorph was the ultimate end result.
Also, the engineer corpses in the other cryo tubes (there were 4) all have their chests burst wide open. It would seem pretty obvious to me some aliens got loose thousands of years ago on that planet, and that's why all the engineers were dead, and running from something horrible in the holographic recordings.
3. I didn't mind it. I like Guy Pearce and thought he nailed the character. There were also deleted scenes with a young Weyland.
4. David was the one who knew how to fly the ship. And we don't know if she put him back together. Maybe the sequel is Dr. Shaw and David, The Android Head having adventures.
