You hear that there are noises coming from a long-abandoned prison nearby. You go to investigate and after fighting a few undead and skeletons, you come across a prisoner who is surprisingly still alive. It turns out long ago, a wizard cast a spell on the prisoner so that his empty cell remains locked forever with no ability to unlock it whatsoever, and what's worse is that the prisoner can't die, but can feel all sorts of feelings such as hunger and thirst and pain. So the prisoner asks the character to go back in time using an item the wizard left behind in the warden's room to a time before the arrival of the wizard, and kill the prisoner's past self so that he dies in the present, ridding him of his suffering, since this is the only way to save him.

Something involving snatching a dragon egg from a lair...

I'd like to see a bunch of quests where you serve under a master of an art to learn more. For example, I would love to meet and ex-member of the mages guild who was a theoretical study sort of person who could teach you academic necromancy (stuff like reanimation, channeling souls from creatures rather than humans). He would teach you a view of necromancy that was based around preventing death or bring people back from the brink (like an emperor or something) but you would have the ability to take this as a good player or an evil one. However, there would be an option to also join less responsible people and perhaps be captured by bandits and earn their respect and become a member of the faction.

You got something going with this. This could really help with the Master trainers. giving each mastery a greater perk and a backstory to obtaining it really sounds good.
This is why I think working with Factions could be more important than ever, what if this ex member still had contacts that he still checked in with every so often in the guild that you could persuade to put a good word in for you or to reveal their location?

I want whodunit.

A noble man sends you on a mission to kill the "Orks who saw Waaagh!"

When you try to reason with them they say nothing but "Waaagh!"
And then you kill them.

You would first notice that as you wander about, the colors would fade and the music would soften. You then notice a small settlement, and as you enter the town proper the music would be silent and the town would be fully grayscale.You enter the town, only to find the town completely abandoned. Everything appears intact; food is on tables, freshly chopped wood, and candles freshly burnt. In the center of the town is a small castle of sorts. As you search the castle, you find a small diary on the throne, detailing how a strange man, with a gray beard and a staff came to the town one afternoon. He was as charismatic as he was insane, and managed to convince the count of the town, the authors father, that he is a prince from a far off land. He was trying to coordinate a deal with the count of some kind. The author, a young girl, seemed to be the only person immune to his charms, and remembers that before her mother passed she handed her an amulet to the author, warning her daughter of a deal she made a deal with a daedric prince and that the amulet would protect her from his magics. Now scrawled hastily, she writes about being ready to confront this man with an accusation.

Armed with the dairy and finding no answers in the town itself, you would set off for the most nearby settlement. After talking to the people there you would realize that everyone is hiding something. If you are well liked enough, you will be pointed to the town lunatic. If you talk to her, she will rant about her youth. She says she was the daughter of the count of (town name). Presented with the diary, she will burst into tears. She will call you a liar, say that you are a delusion. She will then run off (you will be held still as you watch her run). If you return to the town, you will instead find a meadow, with her corpse in the center of the clearing. Once you progress far enough into the clearing, Sheogorath would approach you (the bearded man from the diary entry). He is smiling, and offers the amulet if you keep their meeting and the events you witnessed a secret. He emphasizes that you have no option in the matter, and poofs away. On the woman's corpse you would find the amulet, which would give resistance to magic (enough to make a Breton immune to magic altogether).