Along with 'Lost,' Lindelof has written the revamped 2009 'Star Trek' as well as the upcoming 'Cowboys and Aliens' directed by Jon Favreau. Thus, he's no stranger to writing science fiction. He's even written an 'Ultimate Hulk vs. Wolverine' mini-series for Marvel Comics. Actually, it's a wonder he hasn't been tapped for one of the upcoming Marvel Comics movies. Perhaps in the future.
Most likely, Fox is trying to use this opportunity to reboot the 'Alien' franchise just like the 'Predator' franchise was recently redone (and the 'Star Trek' franchise, and a myriad of other franchises). It shows a lot of faith to give the concept back to its original director to reimagine it. Hopefully it won't result in a big pile of suck.