1) The main issue seems to be that most VNs consider the moral values of the protagonist and not your own. Well, think about this for a moment: what determines one's moral values and principles in the first place? Isn't that his/her own past experiences? If every given choice reflecting moral principles has to be picked by you, wouldn't that mean that the protagonist himself has no integrity of his own? What most VNs do is provide you with a point of view of an individual whose moral values are already established. It's obvious that at this point what's left for you is only to pick the route of the heroine you're interested in. Even though at this point, if protagonist's personal past experiences are influencing his choices regarding morality, it'd make pretty good sense if they'd influence his choice in picking a heroine as well (but I guess that'd be too much of restricting).
2) I think this is the main point:
It may not be impossible, but it'd probably require tremendous amount of planning, writing and recording. Which in the end would amount to a significant budget required for the production. Especially if you're talking about major events happening after picking various choices - imagine how many different routes and endings it'd require. It's also true that not everyone enjoys pondering about such philosophical matters. Even aside from Moege, if the author has a moral message to deliver, it's enough to do so with plain writing. Such questions may be able to add a certain spice to the story, but it'd be troublesome if they were to affect the story and the ending in particular. You said it yourself, there's no right or wrong when it comes to them. So why does one has to end up with a bad ending after answering such a question? And if they weren't, wouldn't people consider them useless?
3) It would certainly be more realistic, but I'd make me replay the same pieces over and over again. I hate the idea. I like intuitive choices and I hate the ones that are not - especially if they determine the ending I end up getting. For that reason I also dislike "Go to location A / B / C / D, which will make you meet heroine A / B / C / D" principle if I don't know what I end up with.
4) It's meaningful and meaningless at the same time. Meaningful, because it'd be able to create a more immersive experience. Meaningless, because it'd only be immersive for the first time. The player can always revert to a previous save file and go through the same thing, this time already knowing what's awaiting for him. Again, it'd probably be more realistic but I dislike the idea because the choice is not intuitive. Save the children and die protecting them? Save the mother and be killed by her? Save none and be abandoned by the others? It'd require you to go back every time you realize it's leading you to the ending you don't want to get. I'd rather have a protagonist making a wrong choice by himself and get a "sad" ending rather than going back later and replay the same piece again to get that particular good ending. It ruins the immersion for me.