Blanket black and white morality systems are so cliche. Radiant AI sounds much better since an NPC has it's own dispositions I imagine you can get away with murder if the NPC likes you enough. I would kind of hope NPC's have their own sort of ethics programmed without having to befriend them. where some might go nuts if they catch you stealing others might not care enough to bother telling the guards.
Morality systems are so stupid like say you break into someones house how is that a bad act in a game where that house was programmed for you to go into but you're some bad guy cause you went in at the wrong time or under the wrong pretenses?
I have to admit I liked Morrowinds faction system because the different factions had their own codes although some rules tend to be rather universal take the factions in Oblivion you could just add 'to do so is to invoke the wrath of sithis' quote to the end of every guilds rules like say the fighters guild and even though they take no criminals they would sound just like the rules of the night mothers guild.

I like the idea but leave the Karma type quests in Fallout. Plus I think the Radiant AI story will give us unique quests depending on what we have done in the past.

I could see tracking "good" and "evil" acts seperately:

A character who does several "good" acts, by helping out an NPC without reward, or doing something that's beneficial at a risk or cost to themself, would be viewed as "good".

A character who does "evil" acts, by acting in their own interest at the expense of others, would be viewed as "evil".

A character who only does "good" acts for sufficient pay, or does neither "good" nor "evil" acts, would be veiwed as "neutral".

A character who does both "good" and "evil" acts would be viewed with some suspicion as "chaotic".

A character who does "evil" acts purely for the sake of doing evil would be viewed as "criminally insane".

Slaves are only accepted in Morrowind...

Probably reputation, thief guild gave higher infamy than dark brotherhood, in a reputation view it makes sense as the thief guild is far less secret so rumours goes around.
The guards knew Armand Christopher was a boss in the thief guild but could not prove anything.

I Would say thats either Morally ambiguous or Ethically subjective. Not neccisarily nuetural. Because Good and bad are all a matter of perceptive. Nuetrual Is more like taking the middle ground not good or bad. Like a consciencious objector. Too deep?

There are no good or evil, only mutual, neutral, parasitic, or destructive relationships. Shades of gray. What one side sees as "evil" the other side sees as an act of bravery or prowess.

Yeah, but that should go to the guild as whole.
No one should know that you are a member of Thief Guild/Dark Brotherhood (unless you get your cover blown somehow) and you shouldn't directly gain infamy for what the guild did, if you get my point.