It might have been mentioned before, but here's what I'd like to see in Prey 2 (which I am really looking forward to btw
):
a) Less linear levels (DOOM1/2/DN3D-style, nothing more)
b) *More extensive use of portals
*Spatial Anomaly in The Complex - more stuff like this, please
c) More puzzles like Cube in The Complex
d) No isolated-arena run-and-shot-until-it's-dead boss battles