From the game's director:
We spoke about the subject with Raphael Colantonio at QuakeCon this past weekend, and he says that the thematic elements are similar enough for the games to share the name.
"Well it was a matter of, first of all it's hard to find a name for a game, and it's a good name--sounds good," he says. "I think the association that people have about Prey is that it's about aliens on a space station, and it's a first-person game. When we were done with Dishonored, part of the team did Dishonored 2, and the other part [of Arkane]... we wanted to do another one of those games that we usually do, which are in first-person, with depth and simulation and narration, all that.
http://www.gamespot.com/articles/pr...n-unrelated/1100-6442447/?ftag=GSS-05-10aaa0b"This time we wanted to make it on a space station, with aliens, and you had to survive with the full ecology, etc. As we started it, the name was available, and the connections were easy to be made. We just thought, 'Okay, makes sense,' so there we go."
He adds, "[T]he high level concept is similar enough that it made sense to do that."
Previously, Colantonio said that the new Prey has no direct connection to 2006's Prey. "Prey is not a sequel. It's not a remake. It has no tie with the original," he said in a video. "You have to look at it like a reimagining of the idea."