D&D provides a terrible moral compass.
To think that the mechanics of D&D, most notably the alignment system, provide any real lesson to anyone is ridiculous. (Note, however, that roleplaying itself is very good for improving social skills, cirtical thinking, etc.) It's jsut general entertainment value, and with it, fun. You kill monsters, you get treasure, you achieve greatness with a character with a straightjacketed ideology. Some lessons you get from the PHB and the DMG.
I'll just say that Gez hit it right on the head with this one. The fact that there is an alignment system makes many people think in a more biased black-and-white (game-wise) and make many NPCs far less fleshed out than they should, at least, in my opinion.
Deep-immersion storytelling with rights and wrongs in "the big gray" is really good for gaming, but in that case, you don't have to use D&D for this one.
IMHO, for D&D to become "deeper" story-wise, you have to abolish the alignment system. It feels like a straightjacket for how the characters should act. For example, how is slavery (in an ancient historical-fantasy world) defined? Should a country be lawful evil just because they condone slavery? From that, the cliched newbie would slaughter every guard just becaue they follow slavery and are thus "evil". There are many, many arguments in what is right and what is wrong, and the alignment system makes it feel like a one-way street. The yin believes in angels, so the yang must believe in devils and be demon worshippers. (Or axiomatic and anarchic, or however law and chaos are defined.) Life is too complex to really use nine levels of character, with a few small side traits.
It is utterly impossible to use alignment in modern games (D20 Modern?). Is George W. Bush lawful good? Some Americans say yes. Is GWB lawful neutral/evil? Some Europeans say yes. Is GWB chaotic evil? Some Middle Eastern Islamists say yes. Here, alignment just has to go out the door. Traits, beliefs, and nationalities are what is gold here.
Now, if you want great good attacking the infernals this side of Sauron or Takhisis (sp?), go on ahead. But it could get pretty boring beyond an arcade-like video game, and we need depth.