I really wanted to be able to actually give the Companions a choice. Say "Hey, I have like 3 of these hag heads...I could cure you!". I can't remember how many Lycanthropes there were in that guild but I think if you count the player, it was more than the 4 hags you could kill. Which means you'd have to leave somebody trapped as a Lycanthrope. Seriously, that would of been a pretty interesting moral dilemma: Do you cure as many of them as you can, but not yourself? Do you cure yourself and leave one of them cursed? Do some of them even want to be cured, or do you force it on them?
Plus yeah, ever since Bethesda realised "We can just make it so you can't kill certain fuckers" the plots have just become railroaded messes...and they were never exactly off-rails to begin with (said it before, one of my favourite Morrowind mods is the one that made it possible to join Dagoth Ur and even betray him, separate the Tribunal from the heart and become the one true god of Morrowind. All whilst keeping a good deal of moral ambiguity and presenting a lot of choices and paths you can take).
I'd love to see what Obsidian Entertainment could do with Skyrim's engine. New Vegas is one of my favourite open world games ever because of the emphasis on choices and story without leading you around by the karma meter. Leading the player around by the Karma meter is my main complaint of Bioware games, a lack of emphasis on choices of Bethesda games (they tend to provide one or two at big moments, but overall it's always been rather rail-roaded).