In short, I'm very unhappy with the Vanilla Main Quest and the faction quests. (With the possible exception of the Dark Brotherhood questline). It's not that they are too easy, I know what to do about that. It's that, especially compared to Shivering Isles or the work of modders, they are just dull. They seem too unsophisticated and so linear it's mind blowing.
For an example, consider the Mages Guild. It seemed obvious to me pretty early on when I first played, that the Guild was inhabited by a fair few less than competent members and that Traven was a complete fool. As the quest progressed, I was at least hoping for an explanation of what he had against necromancy that he was prepared to gut his Guild for, but haven't found one in game yet. So what I'd like would be something different. Maybe the option to join or form a third faction. Dedicating to deposing the buffoon Traven, restoring the Guild and then fighting off the Necromancers that Traven so artfully recruited for.
I'd like to see a degree of sophistication added to all the main Quests. Normally I know people are reluctant to do this, but I really do think they need something added. Of course, recommendations for Guild mods post completion are also welcome. I've heard of a few, but can't find unequivocal reviews of any.
Normally, I can find what I want without bothering people, but I'm a bit stumped here.