Bethesda has reiterated time and time again that their upcoming Prey game is not a sequel and it’s not a reboot of the original title. They recently explained what fans should expect from the game, but the question remains as to why they are using the name “Prey” at all if it has nothing to do with the original game or canceled sequel.
According to Raphael Colantino, Creative Director at Arkane Studios, the theme of the two games are similar enough for the new Prey to keep the Prey 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. 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. 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.
[T]he high level concept is similar enough that it made sense to do that.

And I’m sure Colantonio doesn’t want to discuss what the new Prey game is ever again.
When he discussed what to ...