Let's look at Oblivion: What's the central conflict? Mehrunes Dagon vs. Tamriel. But what about the major side conflict? There isn't one. Instead, we get various Guilds and quest arcs with designated: Good, Evil, and Neutral. So a good holy Knight character wouldn't do the Dark Brotherhood but instead do a certain quest arc.
Granted, Oblivion did have a great story. But it's very clear cut and differences between character in terms of what quests and story is almost always standard. Good characters do this and bad characters do that.
~~~~~~~~~~~~~~~~~~
Fast Forward to Fallout 3 and we see the same thing. The Main Conflict is Brotherhood vs. Enclave. The big moral decision is whether or not to blow up Megaton and whether or not to poison the water supply. Evil players will almost always opt for destroying Megaton and good players would opt for saving it. Same with water supply.
~~~~~~~~~~~~~~~~~~
And now Skyrim. I'm skipping New Vegas since I could go on and on about the same thing I'm going to say for Skyrim. What's the main conflict? You vs. Alduin. But what are the major side conflicts?
Well the biggest one is the Civil War and that's where we hit a standstill. Think long and hard about what the Imperials and Stormcloaks represent.
Neither side is good, nor evil. One can argue just as well that the Stormcloaks are good and the Imperials are evil as I can argue the opposite. And that's where Skyrim got it right. A moral choice that isn't about good or evil. Isn't about the right thing to do.
This is what Skyrim did right. Just like how in the real world, political parties aren't good or evil, merely how your ideological values fall into respective political parties, Skyrim emulates that perfectly. Your ideological values and the perception of dialogue with the characters will influence which faction you will side with.
And that's not all. We then have the Blades vs. Greybeards. Are you in favor of mercy or justice? Mercy isn't always good and justice isn't always evil. But more importantly, what are your perceptions of morality itself? That's what Skyrim did right.
Until you actually play the quests. Then you see what Skyrim did wrong.

