It's been discussed in many other threads by many people, but I'll try to sum it up.
Thanks very much.
I agree with you on every example you gave.
As I've mentioned before, I am really enjoying the game. But, I have had the same thoughts you mentioned.
My experience with TES is limited to Oblivion and Skyrim.
The whole "head of the guild" thing in Oblivion ... and now Skyrim ... didn't really work for me logic-wise for the reasons you mentioned. I enter the guild as a noob and after completing a few missions given to me by more senior members, I'm suddenly head of the guild and leader of those senior ... and presumably far more experienced ... members.
Now if during the course of the guild quests the more senior members retired or left the organization feet first and by the end of the final quest I ended up being the senior member of the guild or during the course of the quests I was found to have some unique ability that made me the obvious choice for guild master, being elevated to that position would make sense to me.
However, that isn't the case and I found myself wondering exactly what it was that qualified me for the position.
And in all honesty, if I'd been asked whether I wanted to be guild master or not, I would have said no if I didn't believe I was ... at that point in the game ... qualified for the job.
Now the obvious retort is that if I didn't want to be guild master, I shouldn't have joined the guild in the first place ... or just not have completed the final mission.
However, that doesn't address my issue, which is that if want to complete the guild quests and maybe become guild master master, I'd like to believe something makes me more qualified for the job than any other member ... and I mean something other than the mumbo-jumbo opinion of, for example, a Psijic monk.
And it would be nice to have some actual duties as guild master, rather than the life goes on without you if you never visit the guild HQ again.
As concerns Skyrim specific stuff, I probably wouldn't have gone with the "civil war" idea at all and if I did, I would have provided a third option for players who don't think either the Stormcloaks or the Empire in it's current mollify the Thalmor condition are necessarily good for Skyrim.
Other "illogical" things I ran into was finding DB assassins after me pretty much from the get go, then being able to join the DB without any qualms on their part, e.g., "Sorry, we have a contract to kill you". On my latest character, I have Thalmor trying to kill me even though I'd had no interaction with them up to this point ... haven't even visited the Greybeards ... and I have to wonder why. I've run into a guy who called me the "champion of Nomura" even though I ended that quest rather abruptly in the Markarth hall of the dead.
You said, "Everyone is telling you the end of the world is near and that you need to rush rush rush.".
I've found this to be pretty much a staple in the RPGs ... admittedly few in the last ten years or so .... I've played. There's always some (phony) element of urgency that we all know can be ignored ... because the world won't end regardless of how long it takes for us to get around to finishing the quest.
If "urgency" is part of the story, it should be "real" and it would be interesting for it to have a real "consequence, e.g., I dawdle around doing whatever rather than immediately doing what was necessary to deal with Alduin and at some point, the world does actually end.
Would likely piss off more than one player though, particularly if their only option was to restart with a new character.
Re: FNV "consequences", I agree with your thoughts however, I can see where others might not. There was a thread a while back where the OP was grousing about the fact that they'd sold their Thieves Guild armor and then discovered they couldn't upgrade without it.
I'm the type of player that hangs on to anything that seems unusual or special in some way, so I didn't run into this issue myself and I don't need the type of "you can't store or sell quest items" logic that is in the game for some quest related items.
Taking this type of option out of the game wouldn't bother me a bit however, from Bethesda's perspective probably reduces the number of enraged email and/or forum posts from players screeching about how the game should have told them that the item they chose to sell was required to, for example, complete a quest.
Same thing with "invincible" NPCs. I can understand the rationale of keeping quest critical NPCs "invincible" in respect of other NPCs however, not so much in respect of the player.
If, for example, I decide to knock off someone like Maven the first time she gives me a snotty response, I think I should be able to.
If that results in unexpected consequences, e.g., entire thieves guild is now after me and/or I find that now I can't join the thieves guild well, too bad, so sad for me.
But again, I'd expect lots of sqawking from some players.
I'd say it's definitely easier avoid some of the above-mentioned issues in a linear game in which all players have pretty much the same experience and are herded along by the game than it is in an open world game where for the most part people can play the way they want.
And I think that no matter what Bethesda does, some players will complain that it has impacted "the way they want to play.
However, if Bethesda can clean up some of the more egregious stuff, it will provide a better overall experience for the majority of players.