It had everything: a cohesive plot, good characters, good actors to play those characters, kick arse special effects.
Very rarely have I seen a prequel I actually enjoyed, but this one is superb. I think, because unlike most prequels it was not just showing us something we already knew. Prometheus not only takes the viewer into the origin of the alien species, but the human species as well. It also has a lot of mirroring of the other films in interesting ways.
The whole aliens made us idea is not new, but the way Prometheus approached it was highly entertaining and just different enough to make it very interesting. Beautiful sequel at the start introducing them as well.
Michael Fassbender is utterly brilliant as David. He's all kinds of hot and yet utterly creepy at the same time. He had a whole 'OMG pretty, but wow there's something missing' thing going on that is just perfect for his portrayal of an android.
Idris Elba is also brilliant as the captain of the space ship. He has some great lines and plays down to earth with a side of heroic human really well. He's practical, but not bitter like we have seen in some captains in gritty sci-fi.
Then there's Charlize Theron as Meredith Vickers, who is almost as cold as David, but with that spark of humanity that makes her seem actually worse. She does a fabulous job of being the corporate bad for most of the movie.
And of course Noomi Rapace as Elizabeth Shaw, who is really the star of the show after David, but didn't actually capture me until about half way through. At the end she definitely shines, but she's no Ripley, sorry.
BELOW THE CUT ARE SPOILERS