Are you really saying that you don't think the ability to play specific background music at different times could increase a story's effect?
Why yes, it can, actually, because in stories, a variety of things tend to happen. Some moments in a story may be happy, some may be aad, some may be intended to make you feel fear, others may be meant to make you nervous, when you can play music that fits the mood of a particular scene, it can help to enhance the mood, and when you have music that blatently conflicts with it. Imagine a light hearted song playing while people are being chased by some sort of horrid monster in a horror movie, or a happy song when someone we're supposed like dies, it doesn't work, unless you're trying to exploit the irony of music that conflicts with what is happening in the story.
So yes, I agree that the Creation Kit should give players the proper tools to easy insert custom music into a quest mod or other mod, if it doesn't already, in fact, the game really should take advantage of this by default, using unique music for certain special locations or events, but modders should also be able to do it themselves, but really, I see no reason to object to ANY proposal that would give modders more freedom, so long as it does not have negative impacts on anything else, such as cases when people are asking Bethesda to sacrifice the quality of the unmodded game to make it more mod-friendly.
Now, I'm not saying we should expect heaps more from mods (although I do, but then again I make them) but if these guys had better tools, they could have made it even better, no?
And yet out of the problems you mentioned, only one of them really has anything to do with tools, the others are design choices.