I have never really liked being the leader of a faction, just because I completed a quest line for that faction. If it is possible, I plan to add options to appoint someone else to lead a faction after the quest line is completed.

Ideally, the player would be able to turn it over to any high ranking member still surviving at the end.

Possible examples that I think would be interesting:

Winterhold College -- Urag gro-Shub
Thieves Guild -- Vex
Companions -- Eorland (would have to persuade him to join first)

I haven't completed the other factions yet and need to see how they play out before coming up with ideas.

I'm open to suggestions for other possible endings as well.