What I could add about the undercity? Check the bards' "Song of the Vatyrs".
The Rhalâta cult were supposed to be the ruler, but they have never been. It's always been the Holy Order. The apothecarii in the undercity works under the Order. And what's most devastating fact is the Order has built a tunnel to release poison gas from the temple to the undercity in case they revolt.
I am strongly impressed by the unfinished locations of the deeper dungeons, the corpse pit, crypts, the orphanage, the glimmerdust lane, spider princess' lair. The quests and things related to the lore had to be cut out of the project. I strongly believe there are stories written about the vatyrs in the orphange, the spider queen, the Darkhand family (which are lost ones that use magic with Dragon Priest animation), the drugs and supposedly street fighting. There must be a lot of story behind this.