Actually, so far I'm finding Skyrim to have pretty good moral choices. Granted, I'm only 9 hours into the game (and in Skyrim that's not much), but I've already found myself in some pretty tricky situations.
Someone tells me that assassins are after her because of a crime she didn't commit. I track down the leader and he laughs, says they're not assassins, that the woman is lying to me, a horrible criminal, and that I can help him catch her and take her back home for a fair trial. I agree to do it, but then have a change of heart and kill him instead. I have no idea if this will have an impact on the game world as a whole, but it feels significant, and I have no idea which one of them was lying. I had to go with my gut. That guy is dead now, and the woman is still walking the streets.
In the middle of all this, a random guy runs up to me, shoves an enchanted weapon into my hand, and demands that I hold it for him for a minute. Seconds later I see another guy running around screaming "Thief! I'll kill you!" The guy runs up to me, asks if I've seen a thief around here. Do I rat him out? Tell the truth? Give the weapon back and hope for a reward?
Then there are larger issues. I walk into a city for the first time and see a guy about to be beheaded for mistakenly opening the gates to someone who planned on attacking the king. The crowd seems uncertain about whether he really deserves to die for this. Do I stand by and watch it happen? I could run up, kill the guards, and save the guy. I'm strong enough that I'm pretty sure I could do that and get away. But then I'd be a criminal here, probably could never do anything peacefully in this city again.
There have even been times I've seen bandits, wolves, and other NPCs that are usually enemies, but they haven't attacked me. Do I kill them anyway? Let them live? Or, I see a pack of wolves hunting an elk. Kill the wolves and save the elk? Let them go, let nature do its thing?
I meet an orc on the side of the road who informs me he's looking for a glorious death. Should I kill him?
Then there's the larger plot issue of the war. I can take a side, or try to stay out of politics.
All this is done without morality bars or points. I think the real problem with moral choices in games is they're always trying to quantify it, when they start calling it a "morality system." Systems break the realism. They get you thinking about how to make the bars fill up rather than letting you get immersed in the story. As you say, it should be invisible to the player, otherwise it becomes just another points system to min/max. I much prefer when the consequences are not counted up and presented to you. Just there, in the world, in your mind. That person you killed never comes back to life. You can't go back and make the right choice when it's too late.