I think Lindelof was quoted as saying a sequel could actually go further away from Alien rather than closer to it.
But I think the more I come to the opinion it was not meant to be a direct prequel (it sorta is, but we're probably going to be going the long route before we get anywhere near LV426 - if that is even part of the equation) the more I like it. But the film suffers because they couldn't let go of it entirely and trust the separate idea they had.
'If the Apocalypse starts, beep me!' - Buffy Summers
'The sky's the limit.....' Jean-Luc Picard, 'All Good Things'
courtesy of Saquist