There's a Ken Levine Q&A on GamePro, asking BioShock's creative director about development of that game.
This sounds really open-ended, but in a nutshell what do you think game designers are doing right, and what do you think they are doing wrong?
KL: In a nutshell they are giving gamers more freedom and they are not spoon-feeding them their stories with walkthroughs. They are opening things up for the gamer and that is the future of games; it is freedom. I think what we are doing is a lot more right, than what we've been wrong.
YESSS! This is what I tried (and failed) to convey in that "Micromanagement / Gofer Factor" thread. Game designers need to concentrate on giving the player more freedom, but to gently influence their decisions toward the intended goal. This would be more intuitive and satisfying than just plopping down a waypoint, having an NPC say "Go here", and then script a number of enemies to try and enforce that command of "Go here". Bioshock's level design offered exploration, and even though there were waypoints, there were places to explore.
Instead of giving a huge list of what the player must do, allow them to explore, to discover the story for themselves. The non-narrative parts of HL2, Bioshock, and Doom 3 were geared for this. Instead of having orders shouted at the player, they found clues, observed the environment, and pieced together the story for themselves.