For example: The whole thing with the Khaza staff.
After the spider caves, you can't get through a plot door without a maguffin. Ok. That's fine. That's a staple of videogames I don't have a problem with.
But the plot door is literally a bunch of sticks and hides and far weaker than the doors you've broken down before. So you kill your way through goatmen to recover their stolen/lost staff to later present to them as a peace offering to let you travel through their territory. These are the same Khaza/goatmen (demons of Baal in D2) that the nephlem dismisses as being unimportant and an obstacle to be casually killed in an earlier quest for the first sword piece.
Because YOU can't possibly knock down their sticks and kill your way through them. THEY have to knock down their sticks so you can kill your way through them... O.o
You could have exactly the same gameplay and remove the plot hole by changing a couple of lines. The goatmen's magic controls the normal animals so the cultists are controlling the goatmen with the staff/maguffin. Break the maguffin and the cultists lose control. Everything still continues to attack you but at least now there's an in game reason why everything gangs up on the player, but doesn't attack each other. Plot gate opens because cultists are dead.
Or another example:
Skeleton King's crown (the one that was a 100% quest drop in Diablo 1 and some adventurer took/sold to a merchant) is needed to open the door next to where you first meet Cain. mkay.
But you also need the crown to place on the intact skeleton left sitting on the throne. Which is apparently the same bunch of bones destroyed in Diablo 1 to awaken the already awake and incorporeal skeleton king... so you can kick over the throne and get through the door under it to the crater which is your actual goal. Which you couldn't do with the inanimate bones on the throne. Guess they were heavy or something.
Instead the crown/bones don't even have to be there. The SK could hold his ground in that room because you're messing with his throne and he doesn't like anyone doing that.
It doesn't fix other issues like why the Prime Evil of Sin and =tactics= is attacking the most fortified keep anywhere in order to get the black soulstone that isn't there yet. Which you either arrive at after it's besieged for weeks through the hordes of demons, or before it's besieged and stand on top of admiring the view of the battle for weeks. (I still can't quite figure which one it was.) But you eventually help by fire = good. Makes men happy seeing fire? As opposed to putting out fires and raising flags that say "This part of the keep is safe, keep fighting and I'll get to your part next."
The game is full of this stuff. And all it is just yellowkeycard in the yellowdoor. But instead yellowcat into the yelllowpillow. With just a few minor changes it could actually make some sense while keeping exactly the same gameplay.
Though you're absolutely right not to let the players have a rope in Act 1. Skipping half of Act 1 with a simple and common item like that would have been bad too.
I guess what I'm really saying:
I'd like a button to turn off the story. Just let me kill what I want to kill in the order I want to kill it. Even if I'm killing Kuel before Magda. The more I have to go through each distinct quest/chapter with nonsense objectives on the right side of screen, the more it's bothering me.