I've recently been playing through the guilds again for Morrowind and Oblivion, and one thing I have been thinking about is how, especially in Oblivion, there is a lack of choice. A guild is a member of proffesionals, and you are a sort of mercenary in this guild, except for the Mages Guild. You should have the option to pick and possibly decline missions therefore. An assassin doesn't neccesarily have to accept his mission, he can decline it on moral standards because it might involve killing a member of a cause he is sympathetic to, or because he thinks that is a waste of his time. Also, if you can decline missions, if you do a mission it should have possible rewards or repercussions. For instance, you could choose to accept a mission defending a Mages Guild member who is exploring a Daedric temple, which would boost your reputation with them, or you could accept a mission to rob the Mages Guild, reducing your reputation with them. If you declined a mission, this would be the no consequence route, but it might be hard to advance in the guild if you are too picky with missions. Of course, this would require a large amount of possible missions and for there to be randomly generated missions.
Secondly, I would like for the guilds to be a lot harder to advance through. It should involve getting a good disposition with the person who will promote you, doing a lot more missions than previously, and also the skill/attribute requirements of Morrowind. It prevented a thief like me from becoming the Archmage. There was a thread a while back which talked about using in game tests instead of a skill check. I mean something along the lines of, you must open a magically locked box using a spell, or you can choose to train a novice in one of the guilds skills, and if you are not skilled enough you cannot train him.
Finally, I would like more end content after you become leader of the guild. In all of the games, becoming leader of the guild meant you were done. No more missions. As leader of the guild, you should have MORE duties and possibilities. When you become the leader, you shouldn't be sort of shrugged off and told you don't need to do anything, you should have to recruit others or help on a particularly difficult mission.