In an interview with with GameSpot at QuakeCon, Pete Hines, Bethesda's Vice President of Marketing, explained why Prey 2 was cancelled. The answer is pretty simple actually:

"I mean, honestly, it's really not that complicated. It hit a point where it wasn't shaping up to be what we wanted and there didn't seem to be a clear path to get to where we thought it needed to be. We decided the best thing to do was just to not proceed. That's just it."

He also commented that he does not think Bethesda will ever go into more detail about the situation, as it is all in the past.

" I don't want to go through and talk about stuff like, well, he said this and we said that. I want those guys [Human Head] to have every success and to not have to keep bringing up this thing. Games get cancelled. It happens. Marriages go bad. It happens."

All is not lost for the series though, as a reboot of the series simply titled Prey is coming to PC, PS4, and Xbox One next year.