I've been touting this for years: I think the split of quest lines before and after becoming head of the guild should be 50%-50%. So you spend half the time getting to the head (which can be accomplished multiple ways in each faction), and then as the head of the guild, you get power and control... and RESPONSIBILITY, in that there will be opportunities and challenges for the faction that you will have to deal with dynamically using your own skills and managing the faction. And each of these challenges can be tackled in different ways that affect how the guild turns out etc.
Example:
Assassin's Guild:
As underling, hatch plot to kill leader and take his place.
As leader, be paranoid and try to foil plot of underling to assassinate you and take your place.
Thieves Guild:
As leader, find out that there is a leak in the guild to the guard -- how would you find out who it is and deal with it?
I am fond of that idea.
But I don't think that should be a designated quest, that should be a burden that follows you throughout the game,
DUE to the fact that you're the leader of the assassin's guild.
There should be random quests generated to designate assassination attempts against your character led by a random NPC underling that is in your guild.
But there should be different challenges like this for each guild.
Fighter's guild- You will be challenged to a duel (assuming your followers approve of you) or they will attempt mutiny due to your bad actions. (random quest generator)
Thieves guild- A contest to steal an item within a certain amount of time, or an archery contest, or a duel. (same as others).
This feature would dramatically add character to the factions.