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.