Expanded storylines for the Guilds, and by expanded I mean story lines that aren't pure drivel. The guilds had some sparks of ideas but never actually capitilized on any of them.
Fighters Guild:
Would have been better that werewolves in Skyrim were wild beasts not just located in the quests. That way you could also have a bunch of quests that focus on the Were companions hunting out of control werewolves in order to safe guard their homeland. And have a select few missions where the were in question joins the companions *see below story* and become a follower, when you shift they do aswell to give you a sense of comradery.
* You get sent on a mission to find another out of control werewolf and to kill it. You find that its targeting a specific family in a farming community.
- Option 1 - Kill the werewolf mission ends with you getting paid by the farmers for ridding they're farmlands of the beast.
- Option 2 - Investigate why it's only going after the one farm hold, discover that the farm used to belong to the werewolves parents but they died under suspicous circemstances. You figure out that it was the current farmers living their (Husband and Wife) that murdered them and faked a deed of ownership.
In order for you to conclude the 2nd option you either have to let the werewolf kill the people then join the companions or use a persuasion check to convince him/her to let them live so that they can rot in jail like they deserve.
College of Winterhold:
Make a long (8-15 missions) quest chain where the college helps Winterhold rebuild earning some trust of the people back not only in Winterhold but all of Skyrim. Imagine seeing each of the mages use their abilites to help people out. A smithy making tools with an flame atronach keeping the forge burning. The destruction mage teacher clearing the land of snow, rock and trees where a new building is going to go. The restoration mage (the one who always complains about people underestimating her skills use) erecting a huge ward over the town so people can work without freezing in the blizzard that rages outside the ward.
Thieves Guild:
To prove their reputation and make it known that they have truly returned to form you embark upon a quest chain to replicate what happened in the elder scrolls book http://www.uesp.net/wiki/Oblivion:Purloined_Shadows. The quest involves stealing several items scattered Skyrim.
The thieves guild chooses to honor Nocturnal on the aniversary of Emer Dareloth, the first guildmaster theft of the Grey Cowl of Nocturnal by stealing into another Daedra Lords realm and stealing a priceless artifact to present to her at her shrine, she then rewards the guild leader who led the theft with the Bow of Shadows. (When you draw an arrow in the bow you turn invisible but when you release it you lose the cloak)
- Item that opens the door to another Daedra Lords realm.
- Something to hide you from that Lords sight. (from knowing your in their realm)
- A device to store the powerful stolen artifact in to keep it safe and hidden. (its power is a danger to you, also hide it from daedra lord until delivered to Nocturnal.)
Along the way you have to bribe, persuade or threaten to get the information regarding the locations of these items or do a favor to someone in return for the info.