-If we choose to complete the Dark Brotherhood line, our actions at the end are entirely ignored, even if done before the Civil War line; what should have happened is that the result of said actions was applied to the CW quests, thus drastically altering their progression.
Just because an important person dies doesn't mean a nation is crumbled and affected to a large degree. The person that is being killed in that quest isn't really vital in any way for the civil war, but they could have made so it was commented on and had some impact. But not that it drastically changes the progression because in my eyes that is wrong. People will mourn the person, but there are people who will quickly replace him so the effect that is due to your actions will be short term only not huge and change the world around you. But NPC's should have recognized it, it should be talked about and portrayed much better then it is.
-Upon completion of the MQ, nobody really gives a damn, and the Dragons keep right on coming; what should have happened is that the random Dragon attacks entirely ceased, and your reputation is set such that when you speak, people listen.
Then you could conclude the same about bandits, about wildlife etc. I don't know how many wolves and bears I have killed or how many bandits have died so far, but in reality if this had been for real both bear and wolves would be on the brink of extinction by now. Alduin is the main threat the other dragons aren't a real threat compared to him, and seeing this is a game and that the player might just not have gotten all dragon words when they finish main quest it would be a bad idea to remove dragons from the world when Alduin died. I prefer that there is dragons still around, because it would allow me to complete all dragon words should I wish for it, not that I have to find all of them and complete them before I kill Alduin. This all boils down to game design, and removing dragon attacks and dragons when stopping Alduin isn't a good thing to do. If there still was dragons around but they left all cities and people alone it would also feel weird that they suddenly turned into peace loving creatures once Alduin was stopped.
-If you ally with the Forsworn during a certain quest, nothing really changes aside from a few dead perma-bodies (both sides) lying in the streets of Markarth; what should have happened is a drastic shift in your standing with the Forsworn, even to the point where those associated with the folks you freed were allies. Also, an equal shift in Markarth's opinion of you, to the point where every time you set foot in the place it starts a massive fight as all the guards try to bust you for treason (yes, I'm aware of the rep glitch, that doesn't count as it's unintended).
This did disappointed me a bit as I had hoped for more then what happened, it would be a perfect start for a new life as part of the forsworn and helping them in their rise to power.
-Joining a given guild has no consequences as far as obtaining membership, let alone advancement, in another; what should have happened is that joining some guilds either locks out joining others or severely crimps advancement possibilities, as they have oppositional goals and either wouldn't want someone they consider a traitor in their midst or would be highly suspicious of them and wouldn't let them advance to the point where they could do something drastic.
This is pretty much a standard issue with TES, joining guilds and consequences for being member of a opposite guild has never been a main concern with the guilds in TES. In Morrowind I was the top rank of all guilds I could be in. In oblivion I was leader of all guilds also. This is a problem that maybe they will fix with next game, although I do not hold my hopes high for it. I would have loved to see something like that as it had actually meant something about what guild you joined, and how you planned to play your character. Added with a good reputation system you could allow for someone to rise in the ranks, but if an assassin was caught and spotted as not only an assassin and leader of the assassins but also the leader of fighter guild he would be overthrown by the fighter guild. That way if people played their character really careful avoiding detection etc they would be able to join all guilds, but if discovered the consequence would be even bigger.
The guilds have always been a thing that has annoyed me since Daggerfall, the way they work when you are guildmaster simply simply feels a bit pointless. I would love for some micro management of the guilds, maybe get a few choices to choose from and then over time the guild would change based on my choices. The thieves guild seems to have some kind of rebuild phase and it will be interesting to play through it to see how it really is.