Nope. Prey is much, much better than Doom 3 - in fact the third Doom is no where near as good as this "clone."
Could you maybe elaborate on the greatness, instead of throwing out blanket statements one after another?
Prey was better than Doom3 because many of the gameplay mechanics didn't force the character to use something useless (flashlight). Also some of the designs for the weapons and the puzzles were kinda cool (figuring out how to get across a room by going on the right wall, roof, then left wall was interesting). It ran off the Doom3 engine so the characters looked almost vulcan, the characters also had a personality (albeit they were each terrible).
Prey was IMHO a better game than Doom3. But then both were run of the mill shooters.
Being better than Doom 3 doesn't make any game a classic, though. Take for example Farcry, as annoying as the Trigen were, it brought something new to the table(open world shooter) and despite other shortcomings, made it work.
Prey might just as well be Doom 4, it doesn't distinguish itself from the rest of the shooters, I remember it as the corridor shooter with the Native American stuff.