The choices are so obvious and the consequences are so immediate, that it becomes impossible not to consciously exploit the system. Some gamers might find it unfair, but in a way, having the results of your decisions come back to haunt you much later in a game would force players to live with the consequences of their decisions rather than simply reload the game to try another approach. I turned the Mage Tower over to the Templars in the first Dragon Age but I didn't realize just what I'd done until it became too late to go back and change it. It was frustrating to live with that sort of regret but that frustration became an important and satisfying part of my character through the rest of the game.
Having the chance to go back and change your decisions in games makes the consequences of your actions even less significant. The Little Sisters from BioShock are a great example. Not knowing what the difference would be, I decided to go ahead and harvest the first little moppet I captured. The whole experience was so unsettling, what with the flailing and crying and apparently turning into a fish, that I felt I'd made the wrong decision, morally speaking. But while sacrificing one at the start and living with that memory would be a stronger character moment, I knew it would also screw me out of whatever reward was waiting for players who saved all the Little Sisters. By reloading the game, I was able to avoid having to live with the consequence of what I'd done.
While it's a great bit of acting and atmosphere, choosing whether to harvest them or not wound up being pretty meaningless anyway. You're offered a substantial practical reward at the start and have to balance that against whether or not you can live with yourself for taking advantage of these creepy little kids. But by the time you reach the end of the game, the rewards for harvesting them are just about equal with the rewards for not harvesting them. So I played through the whole game adhering to a choice that had no real consequence beyond funneling me to either a "happy" or "unhappy" ending that had the added disappointment of effectively quashing the moral ambiguity that had made the setting so captivating to begin with.