Whilst playing oblivion it sort of bothered me that some quests would compel you to do things that your (RPing) character just wouldn't do. Ex: Your paladin-esque character wants the Ebony Blade (a strong sword for those that don't know). Well Mephala wants you to commit double homicide for you to get it, no ifs ands or buts.
Instead I would like a few more options. Still going with the above example, maybe Mephala still wants you to kill those two people, but instead you have to bring her object X and Y from each of them (as "proof" you killed them) and to get those objects you could 1. Kill them 2. Steal it from them 3. Do them a favor and have them give it to you. I know tricking a god isn't easy but that's just an example I thought of in two seconds; you guys understand what I'm getting at right?
I still think some quests should not have alternative routes. For example if your in the dark brotherhood, you gotta murder your targets and be evil cause you chose to join the Dark Brotherhood. But it bothered me that to get some quest rewards that I wanted I had to do things I didn't want my character to do (and I'm not specifically talking about good vs. bad here). Were you bothered by this? Do you think the whole thing should stay as is or should they change it (I think they're getting at something with Radiant Story)? Do you have any other suggestions?
I agree with your initial idea, I think SOME quests should have different options and different paths that allow you to complete them. Personally, I'd like the main quest to, for the most part, have one major path (or, in the case of Morrowind, a path that is practically the same one but accounts for certain things.)
However, I don't agree with anything you just said. You seem to expect to be able to do EVERYTHING with one character. If you want to make a "good" character and you consider joining the Dark Brotherhood to be "evil" then just don't join ( (and, by the way, the "dark" in Dark Brotherhood is referencing their discretion, not any type of evil or anything like that, they stayed in the "dark" as opposed to the Morag Tong who attacked in the open under the idea of honorable execution.) It doesn't make sense from a roleplaying perspective for your virtuous character to join a guild of malevolent assassins, so why did you do it? That's your fault, not the game's fault. The Ebony Blade was said to be an evil blade as well, why would you want it?