If i had to choose a mission that I would like to see in skyrim, it would defiantly have to be one based of the Salem witches. Like have a extra town that is basically Salem, and have like the crucible going on but skyrim style, and you can either help the people stop the witches or help the witches take over, or get a way or something along those lines
1. A war with the Dominion after completing either the Imperial or Stormcloak questline.
2. Form an alliance with Miraak to help him break free from Hermaeus Mora's grasp and take over Solstheim together.
3. Daedric quest from Jyggalag.
I still have more but these three are my favorite.
I felt i had to comment on this:
The Salem witch trials is actually a really tragic story, and a lesson on mankinds ignorance and superstition. I think it would be very wrong to put those events in a game and have any kind of mission related to witchcraft in it.
To actually answer the topic though, then i'd wish for anything that would expand the companions questline in particular as i think its way too short.
I have to agree with Toveor here. Skyrim 'witches' are fictional, but the Salem trials are a real-life tragic event. Also, real witches (wiccans) are peaceful (wiccan rede) and nothing like the witches we see in Skyrim.
More follower quests would be cool. After hearing Uthgerd's back story the first time, I assumed that I'd be able to help her make amends with the Companions, sadly this was not the case. Also after I destroyed the Dark Brotherhood I was disappointed that I couldn't do the same to the other major guilds. As mentioned, The Companions and Thieves guild both have in-game enemies that I'd like a chance to join. For the Mage College, I figure there could be a group of hot-headed Nords living in Winterhold who want to take them out.