I know it's not a prequel to Alien, that was my point. It should have been and even so it could still stand on its own because all they needed to do to have the movie stand on its own but still be a prequel to Alien were those two changes I mentioned in my spoiler tags. They can make Prometheus 2 if they want to, but if this movie had've set up the events that lead up to Alien then they could've freely explored the other aspects the movie introduced in its sequel and make it run parallel to the events that affect the Nostromo years later.
It's a huge missed opportunity because now everyone is going to expect things to be tied in a neat little bow in the sequel which will end up hurting that sequel more than it helps. If they had done it with this movie, said "okay, there's the connection with Alien, but if we make a sequel it will explore new and unknown territory" that would've been awesome. But they didn't, so now it's just going to get overly complicated and peoples expectations will be screwed with.