Well Sven, I agreed with some of what you said. That is not entirely true. Halflife progressed nicely and the story line just kind of sailed along smoothly. Halflife is a good example of what an FPS single player game should be with a great story line and a few puzzles along the way. I think you described it to be more of a thinking game though.
Lets leave the heavy thinking to RPGs and strategy.
The Masquerade Redemption. That's exactly what that engine sought out to do, and does pretty well. If you ask me the DOOM series has the best single player ive seen. Walk around the corner BOOM take down five monsters in one shot with the super shotgun. A door opens, uh oh a Baron of Hell, so you have to strafe it's projectiles and take it out with a series of SSG shots.