So something I've been trying to figure out, I recently got a dungeon map and went through a handful of dungeons from Minish Cap, and they were MUCH more linear than you'd think.
The first dungeon, deep wood shrine, I'd need to look at my notes to be sure, but I think there were two places where you could take a "wrong turn"- basically going off the linear route designed to get you through. Usually, the more obvious way to go is the right path, but if you took the wrong door (one off in a corner or something), you can only go one or two rooms before you see it's a dead end, and backtracking is very minimal. This gives you an illusion of choice without punishing the player for choosing incorrectly.
What I don't get- did the temple of droplets, the ice dungeon, feel too easy to anyone? Did it feel linear or hand-holdy? I looked over the map a few times and it is literally impossible the go the wrong way. You never have the opportunity to go off the linear path. Granted, it's not a straight line, it twists around itself a little hand has multiple floors, but when you come into a room, there is only one way you can go forward from there.
Anyway, shorter summary- for dungeons, a large amount of linearity might actually be a good thing, but it's important to give the illusion that the player has choices and is in a confusing labyrinth, without actually allowing them to deviate far from the linear path.
I should note, however, that older games (and I've just looked at 2D games), often have less linear dungeons, and linearity decrease is a way to make later dungeons more difficult/intimidating.
Its a great exercise to pull up a dungeon map and a walkthrough and draw the path in, have an overview of how the player will move through the dungeon.