Got the 3D to work.It works for me. Looks like something went wrong with your game install.
Because of the way the developers craft the game, the 3D effect made R3 locations look "volumetric", somewhat on par with KZ3 but darker. KZ3 shows more variety and more Hollywood-style cinematic. R3 is more homely, or more trilling depending on where you are. It's not truly scary but occasionally, I wanted to know "Are they still behind me ?", "Where is that noise coming from ?". Don't go in with a horror game mindset, it's a shooter and you have a weapon wheel. ^_^
EDIT: FPS veterans should play in Difficult mode, and drop difficulty to Normal temporarily if you want.
Reinstalling the game actually didn't help, I had to start the game in 2D mode, play until the first savepoint, exit to main menu, enable 3D, continue from the save and 3D worked from there on.
The 3D doesn't seem quite as good as in KZ3. In R3 I get some severe crosstalk if the weapon aim reticule is on a dark background, also when zooming in on some of the weapons it's harder to aim because there is some double vision which I don't recall KZ3 had.
Also now I'm left with some corrupted data in the games menu. Got rid of the corrupted file in the game data menu, but when I did the rebuild database there appeared the corrupt file in the games menu.
Maybe my HDD is going kaputt, I'm not sure but it feels like game installs are taking longer than before... must make a backup before too late. Thank Sony for PSN+ cloud save!