Three major things bothered me.
The SJ aka Engineers. Not portrayed anything like I expected them to be. I almost forgot the flute thing until somebody brought it up. That was ET like camp. Expected it to be more ghost of the shellish. With the jockey's running everything biomechanical style (kind of like cyborg's interfacing with computers using wireless connections in their bodies or direct physical connections into hardware). I just didn't see them going that chariots of the gods route (I mean it was such a good idea AVP used it.....). I don't think many of us saw them going that direction and was already a bit peeved as soon as it was mentioned in the previews.
I realize this of course is based on initial feeling and my own opinion, but I would've preferred the jockey's regarding us with cold indifference until we snuck into their territory trying to steal their own tech or the black goo.
The Alien. So the black goo end result is the Alien.....yet there is apparantly a zillion different ways to get there. If the end result is not the Alien how did they know to make a mural of it?
The talking head. Like the flute, this part was a "It's so bad I'm going to put it out of my head," moment.
I didn't mind the setup, the characters were mostly filler but David, Vickers and Shaw were good enough to carry the majority of the film, the designs were top notch.
The story and script were sketchy.
I think Jimbo wins handily in the next gen scifi story battle, and I don't hold Avatar in that high of regard.