The 'Engineers' are, in my opinion, brilliant. They are not scary I might add, more eerie but full of mystery. Their look is simple yet amazingly 'alien' in appearance which is in stark contrast to the xenomorph which I think works perfectly.
When the living engineer gets pissed its awesome, you think he's gonna be kind in an 'E.T.' moment then BANG!. His size and build makes you sink in your seat as you worry what on earth he's gonna do, you wouldn't want one these guys on your ass!
I can fully understand the 'Star Trek' remarks, that is one element I didn't really like, the nice clean perfect appearance of everything, very sterile and unused looking. The original 'Alien' film of course was set in a used dirty environment which I think is safe to say everyone liked (much like the classic Star Wars trilogy vs the new Star Wars trilogy). But you have to remember this vessel is a different kind of ship than the 'Nostromo', this is simply a ship for travel, comfort, living and probably exploration.
The 'Nostromo' was a mining ship and of course would have been very dirty, grimy and full of unsightly metal and mechanics. I'm guessing the 'Prometheus' was maybe a new ship, first time in use perhaps and this was her maiden voyage? who knows, maybe we will find out on the DVD.
The one thing that bugged me was the fact the technology on the 'Prometheus' was much more advanced then the 'Nostromo', I think that makes it hard to believe the film is a prequel personally.