Giving the Jockeys any sort of relationship to humans. So basically the entire God-damn plot. The cool thing about the Jockey in the original was them finding this weird, dead alien thing in the middle of nowhere in space. It gave a great sense of awe and mystery, but as something long gone that they happened to stumble upon. Saying "Wait up! Turns out they're every alien conspiracy theorist's wet dream!" is cheap, lazy, and disingenuous to what made the thing effective in the first place. Adding "And they were out to get us!" turns the whole idea into the worst kind of schlock sci-fi.
Alien took a simple, cliché idea, did it as straightforward and unpretentious as they could, and put its effort into coming up with a handful of really neat ideas to make it better than the competition. From what the trailers are showing, Prometheus is taking a simple, cliché idea and just making it look pretty. There doesn't seem to be any innovation, just a lot of cool-looking set pieces.
This all, mercifully, hinges on what little we know. Hopefully more information means less griping.
