If you found Prey better than SS2 that's a valid opinion of course.Horses for courses. To me that like saying if you have played Mario 64, there is nothing new in Mario Odyssey.
Subjectively, I found SS2 to be the superior game.
I'm not saying I wouldn't enjoy a new System Shock game nor that I didn't enjoy Prey (I did until it started dragging on). I just don't think Prey surpassed the games it payed homage to. In fact I think (graphics aside) it wasn't as good in many ways.
For starters the enemy variety was worse. I'm not going to bore you by deconstructing both games, but SS2 did a lot of things really well, whilst Prey does a lot of things well but not to the same standard.