While completely true, that it is impossible to properly convey a human DM via a pre-programmed game, it's not impossible to make a game that relies on those very mechanics enjoyable.

1. A skill check should be made to prevent something bad (like a fight you don't want), to improve a situation that is already determined (request a higher reward), or a specific approach to solve a problem (bribe a guard to let you through).
Out of the three, only the last one can potentially run into problems with a human DM vs pre-programmed game. People don't want to kill Nettie, because they understand her logic, yet if they fail the skill chain, they don't have a choice but to kill her - this wouldn't be NEARLY as big a deal if there was at least one other option to get out that didn't require her death - solving a puzzle or something, i.e. extra effort from the player's part.

2. Not much I can say - tying core(?) story elements without an indication of how to access them is a big design oversight. And the current resting mechanics is something that should be reworked. How? No clue. I have ideas, but those are echoes of what others have said and/or would require significant overhauls to the game - so I won't even try.

3. This. Very much this. I think it would be a good idea to lock out some paths/quests based on where the party decides to go - for example if you find the Gith Patrol before going after Halsin, he'll be dead.

4. As somewhat mentioned before - if the choice is A or B, and B is generally the "bad option" that happens due to something outside of a player's control (random die roll, or worse - a chain of those), then it IS going to seem that we don't have a choice. Give us and option C, hopefully even D, and then this becomes a non-issue.

4. (again) Fully agree that other skills should play a part in social interactions. One option would be to allow a player to select from a list of options for what ability score to use, for Intimidation Strength OR Charisma. Other skills should also be part of social events, like instead of Persuasion, ask an incriminating question and make an Insight roll.

5. 5e doesn't exactly have a circumstantial bonus, but even if it did, the mechanic wouldn't change - it would just automatically reduce the DC and the UI would be the same. Still, this feels like something that should be relatively easy to implement: if Quest: Save Arabella [Complete], then persuasion check DC reduce by 2 in druid camp.

6. I agree that the 5e action economy isn't the most exciting and even limiting (PF2e has an action economy almost identical to that of DOS and feel much more enjoyable), however, that is what the game is and, for better or worse, what I was looking forward to play with.