Linear dungeons arent the issue

[Vulcwen]

People like linear dungeons, they just don't like that they FEEL linear. As soon as there are optional paths to take, people end up disagreeing about the route resulting in frustrations.. unless, an "optional" path is obviously better, or basically picked for you. Toto-rak is one of the most hated dungeons in the game.
I think that shortcuts are really important in dungeon design, it makes people feel smart, but people would naturally agree with the path once they know about it and are capable of taking it (aside from XP runs, but that's not an issue in end-game dungeons).

Basically, add things to jump off from/over to skip mobs, maybe a secret way to enter a different route (like having a bomb enemy use self-destruct near a bunch of rubble). Once a secret is discovered, it soon becomes meta and everyone will use it, but it still makes for more interesting gameplay.

[hakurou46]

Once a secret is discovered, it soon becomes meta and everyone will use it, but it still makes for more interesting gameplay.

You mean like the jump in Haukke Manor? Or sneaking past enemies in Qarn HM?
Because then you get the problem where newer players won't know it. I've seen people kicked for this.
Whenever you introduce, by design och not, any selection into a multiplayer game which affects more than the selector, you'll have people complaining. That's not an issue with the game, but:
I'm going to claim that optional side areas are a much, much better idea than shortcuts. They just create unneeded frustration for minuscule gain.
Mark Brown made a great video on how dungeons in Zelda: The Wind Waker feel nonlinear while remaining perfectly linear. Check if out if you're into game design. (Compare Fractal Continuum, or CT re: returning to earlier parts of the dungeon)