Some points to make (mild spoilers for Alien):
People are complaining about the lack of characterization, especially compared to Alien, putting aside the fact that there were far fewer actors in the 1970s (hence the ones we had were better), I'd like to point something out:
The latter film's failing is that the crew is about five members too large; cut those guys out (especially the two co-pilots) and/or replace them with automation, and then give the larger parts a bit more to do in the film. Janek could have piloted the ship alone in the end, for example, and Vickers could have been the Company rep on the ship (i.e. the one who sees financial opportunity in the Aliens and wants to bring them back), while David could have simply been Weyland's agent (for his personal goals), eliminating his presence from the ship. The one characterization I truly felt was lacking in Prometheus was Holloway, who felt like he was only there to inseminate Shaw. He did need a bit more screen time.
But just like in Alien, we again spend most of out time with three people: Shaw, David and Vickers. It's simply that these people have less to do because they're on a bigger ship with more people. To have less people in Prometheus would have made it stronger, but I still feel the plot is as inventive as Alien.
Is it really the point of a single film to make a journey like the one in Prometheus, and at the end of two hours, we should know Who exactly the Engineers are and why they wanted us dead? That after being told repeatedly that the film is not a direct prequel to Alien, we should see a Xenomorph? That we should be shown exactly why David feels he can destroy human lives in the name of his mission?
I think it's unfair to expect a single, two hour film to raise and answer all of these questions. Look at what you already can infer from the Alien franchise:
-Xenomorphs can take different forms based on the host creature. The classic Xenomorph is from a human, but many different varieties could exist (e.g. the Xenomorph of Alien³ or the creature at the end of Alien: Resurrection, which I'm not sure is technically a Xenomorph). Also, from what we can infer from the previous films, "classic" Xenomorphs did not exist until the one from Kane in Alien, because that one came from an egg laid by a Queen on LV-426. The question that Alien did not answer (and which Prometheus may have answered), is what host that Queen had come from.
-Androids are not to be trusted and may have ulterior motives.
I will grant you that the point about Engineers is new material that Prometheus brings to the table, but that very point is what Scott used to set up a sequel to the film, and to be honest, how do you really answer that question? Whatever answer is ultimately provided would arguably be a let down, because it would be like finding out that our creators truly want to wipe us out and here is why. I find it much more appealing to simply contemplate the idea instead of having the final answer, especially when the revelation of the Engineers themselves (including seeing one alive) and subsequent exposure to the creatures that pre-figured the Xenomorph from Alien (like the Queen that came from the Engineer at the end) is already a lot to see in a single two hour film. Much better to let the question weigh on our minds as a possible sequel comes along which could provide more answers and ask different questions.
To my mind, the only other weak point of Prometheus is the idea that this is a different planet than LV-426, when the Space Jockey and ship position have been conveniently set up on this planet (I think it was LV-223?). On the one hand, if we set aside the convenient ship position, and believe, as Scott says, that we are not setting up the events of Alien, we could then say that somehow the Queen from the Engineer (or her progeny) moved planets, and that there were more Engineer ships on other planets, but on the other hand, given the distress signal and the Space Jockey, it feels more accurate to say that this is the same planet from Alien, and the Queen from the Engineer is the missing link between the creatures in Prometheus and the egg that implanted Kane in Alien. As far as I can remember, though, the only time the planet was labeled in Prometheus was on a ship monitor screen, and if I recall, the label of the planet wasn't given in Alien and only first appeared in Aliens (but I could be wrong), so maybe this is just some sort of small but important error.