But... was system shock 2 really that deep? It's a great game (well the first half) but at its heart was a corridor shooter. It was neat to be able to choose what you were going to shoot down the corridor, but I think to call SS2 a masterpiece and to call bioshock a boring linear shooter isn't quite fair.
I'd argue that, while Bioshock had less boxed-in level design, it was much more linear in terms of level
progression. You could revisit levels in Bioshock but there's practically no reason to do so, unless you missed a little sister and need more Adam. In SS2 there were much more meaningful reasons to revisit levels, such as finding appropriate chemicals to analyse materials or needing to unlock/deactivate something a few floors down in order to open a hatch in engineering (or something similar, it's been a while since I played it). The depth of System Shock 2 comes from how it embraces the idea that you're on a space ship; you're not just going from level A to B to C to D.
That being said, System Shock 1 blows 2 out of the water in terms of organic progression.