Well then for a moment, let's examine when it's good to use keys, when it makes sense in a holistic world.
Dungeons that are:
Goddess Trials for a Hero
Enemy encampments (like Forsaken Fortress or the bokoblin camp outside the Arbiter's Grounds)
Dungeons that are functional buildings that would conceivably have doors that lock (Arbiter's Grounds, Hyrule Castle, Ice Mansion)
Dungeons that, if G-King ruled the world, would not have keys:
Caves that are not main game dungeons
Natural formation dungeons (volcanos, tunnels, semi-natural waterways)
Ancient Temples designed to house something people shouldn't otherwise have access to (places protecting Fused Shadows)
Anything that is not designed to have people more through it as a course of its function
Now I'd like to examine some instances in Zelda games where there has been some game device that was used to inhibit your progress, but was not a key. This does not preclude things in dungeons with keys, just interesting progress restrictors.
Majora's Mask, Snowhead: a giant ice pillar prevents you from reaching other rooms. You have to break it to keep going.
Link's Awakening, Eagle's Tower: Stone Pillars that support the upper levels of the tower. You need to shuffle a wrecking ball about in order to take them down.
Majora's Mask, Stone Tower Temple: flip the room upside down to progress
Majora's Mask, Great Bay Temple: need to change the direction of water flow to make certain paths accessible
Shadow Temple: …practically… every damn thing in the temple doesn't want you to go forward.
Hmm… in fact, that last one seems like a good jumping off point. Let's discuss the Shadow Temple and its sister mini-dungeon, the Well. For its theme, the Well makes sense to have a few keys. It was a dungeon in truth, meant to keep and torture prisoners. It drips (both figuratively and literally) with lore and evidence of this purpose. It also has traps and redundancies in its construction. I'm sure you can all remember the basement full of poison water and Redeads. This makes sense, as it would create a situation where any escapee would likely be killed or recaptured. Missing tiles, terrifying monsters that would offer little threat to jailers (such as Like Likes), invisible passageways that hinder you if you are ignorant of their presence but that help you if you know where they are. Only a few scattered keys exist, and their placement and use make sense. For instance, the Lens of Truth is locked away, but it is an object with a conceivable future need. So it is hidden and protected, but in such a way that someone with the means and need can find and access it.
Meanwhile the Shadow Temple does not boast such utility. It is a place constructed solely for the execution of prisoners and traitors. It makes little sense to have keys, because there is never an instance that the people wandering it should be allowed to progress. So how could we fix that? Well, for starters the barrier for passage can be made almost wholly with redundancy traps. Miss a jump? down into the pit full of bad things. Climb out again and start over. Didn't use the Lens of Truth? Pit. Things. Climb out. Start over. No iron boots? PitThingsClimbAgain. Might it get frustrating? Maybe, if you keep effin' it up. But any more frustrating than spending a half hour backtracking around for a key? Who knows?
The second thing we can do to reinforce this keyless theme is the traps. I mean, Shadow Temple had tons of them but honestly, they were laughable. Spinning blades, spikes, falling things… and they all do like, half a heart? Did anyone ever feel genuinely threatened by them? I mean once you see the twin Reapers deal piffle damage, you can just run through it without really caring. Now, let's say those suckers dealt Iron Knuckle levels of damage… then I imagine after your first misstep they'll have your undivided attention. Turn more rooms into a gauntlet of traps and monsters that significantly inhibit your progress. Then give the player ways to get around those traps, and simply make bypassing them the element that allows passage, instead of bypassing them to find a key that allows passage.
Honestly after thinking about it, it seems that really great, immersive dungeons can be created not just by doing away with keys, but examining whether they make sense in the context of the dungeon's purpose. I'm curious as to what others think.