If they weren't 'linear' before, and turned linear, then that is only because the design decision surrounding the dungeons is a result of how people were playing them. Skipping everything optional and that wasn't in the direct path between the spawn and the first boss, or from boss to boss for that matter.

It's well and good to want less linearity in dungeons, but this is largely just a platitude. The nature and purpose of doing dungeons pretty much erase any incentive to... Not be linear. Unless dungeons can properly incentivize this then it's difficult.

What will it give? Better gear than what you may traditionally get in the dungeon? Rare rewards one can sell for Gil? They've tried this and people couldn't even be bothered to kill 3 extra enemies in Haukke Manor, despite the fact that the room they were blocking offered Fine Varnish, which at the time if it dropped would offer effectively 50-80K Gil.