I'm not much of a modder, however, to anyone who can mod and is looking for a modding project, you might try these ideas.
The Dark BrotherhoodEdit
I was really disappointed when once again, Bethesda left it to the modding community to actually give the Dark Brotherhood a decent ending. Also, most (at least, I haven't tried the College of Winterhold yet) of the factions have had a lasting faction rivalry. The Companions where at war with the Silver Hand, the Civil War was ravaging Skyrim, and the main quest had disagreements between the Blades and the Greybeards. However, the Dark Brotherhood only had a few run ins with the Penitus Oculatus.
Therefore, I believe that, while it would not be an easy task (as the Dark Brotherhood Chronicles demonstrated) a good modding idea would be one to rebuild the Dark brotherhood to it's former glory (At least in Skyrim) with the choice of either maintaining Astrid's new views of the Dark brotherhood (Without the Black Hand and the Tenets etc) or to restore the Black hand and Brotherhood tradition. However, I also stated that a faction rivalry would be desirable. While the Penitus Oculatus would be an obvious opponent to the Brotherhood, players of Morrowind may remember another, much older group of honorable assassins with the longest standing feud with the Brotherhood.
Within Winterhold's Grey Quarter, a group of Dunmer have fled Morrowind's deepest struggle. However, these Dark Elves hold a greater secret than most of the refugees. Worshiping Mephala, a small group of the infamous Morag Tong have been given orders to expand into Skyrim to ensure the Tong's survival. Inevitably this will result in confrontations with the Brotherhood, However, the Tong eventually learns of the Bortherhood's recent weakness, and further orders are given to eliminate them.
I think that the player should be permitted to join either side in the conflict, so as to allow players greater freedom while playing.
If anyone is actually interested in this, it's been started here. http://sdbm.userboard.net/