The only inconsistencies I saw were minor character behavior issues. But those things did not spoil it for me. I noticed one person in this thread didn't like how similar to Alien this movie was, as far as certain things happening and maybe even having a strong central female character. I LOVED that they were able to sculpt a prequel so that it was a story on its own, yet also had those parallels and nods to the 1979 movie.
I loved the look of the pre-human or whatever that guy is. I loved the way the tech of that ship looked and worked.
Stuff like that, as well as what I felt was superior acting, kept me enjoying it. I actually felt like it went by just a bit too fast. That's how good it was for me. I will chime in on 3D. I didn't really notice. For me, so far (with exception of Avatar), 3D has been a waste of time, comfort, and money.
Slightly embarrassed to admit one thing I didn't figure out and want to know: In the very beginning when the badass looking pre-human was standing on the edge of the river and imbibing and changing. I don't understand why he did that, what his intention was, what really happened to him, and how it related to the rest of the story. I've thought of a few potential scenarios but none of them seem to fit completely. Help?