Basically-

I have a theory, that in order for a system of drops to work fluidly and well each kind of level (or at least each kind of action) can only really give one type of reward.

As an example of this theory, gear requires several components-
-Materials = primarily from monsters
-Crowns = primarily from monsters
-Fire crystals = primarily from boxes
-Orbs of alchemy = primarily from boxes

When I go to craft gear, I never need materials because I get enough of those farming crowns from monsters and then have extra left over. When I go to upgrade my gear I never need eternal orbs of alchemy because I find those faster than radiant fire crystals when I earn those farming Dreams and Nightmares and it is always the case that I either need orbs or fire crystals, but never both unless I'm new to the game and just don't have them yet.

So how would I do it exactly?

To solve this issue, I would like to suggest separating all of the loot in the game such that certain levels are far, far heavier in one type of loot than the others. I'm going to go through some of the main levels and mark them with one of the following terms:

This already describes most of the levels in the game so setting it up should be simple-

Levels Marked Crowns
Firestorm Citadel
The Jelly King
Other bosses
Most missions
Operation Crimson Hammer
Danger missions

Levels Marked Loot
Levels that contain bosses/just boxes on the above
Treasure Vault
Shadow Lairs

Levels Marked Crystals
Dreams and Nightmares
Arena
Missions that include an 'arena'
Some of the multi-monster set areas (like scarlet fortress, aurara isles etc.)

Levels Marked Materials
Compounds in the arcade
Single monster-specific areas in the arcade (like decon zone, lichen lair.. etc.)
The daily mission

Levels Marked Orbs
Clockwork tunnels
Special missions with minibosses (sputterspark, Herex)
Some of the multi-monster set areas (like scarlet fortress, aurara isles etc.)

And lastly, levels would have a marker of some sort put on them describing the above categories to let players know what they're in for.

The end result

Players will get what they want and little else, causing them to branch out in where they desire to play, causing them to want to craft more items and explore more.

Most of the levels people do are marked with a 'c' for crowns which would be designed to create tension in the crafting system. All of the sudden you have tons of crowns flooding in and no materials, less orbs, less fire crystals.. suddenly, we're all rich with no way to craft or heat gear except the arcade and a few select missions.

When players want crystals or orbs, they have the option to play missions for those things. The missions they play however will not be generating anything but what they want, and so will not be as well rounded as doing the arcade for these things but less frustrating, as they will find what they are looking for.

The only way to get materials reliably will be the arcade which will also have levels that generate orbs and fire crystals for players that are level hunting. Materials become scarce, players become hungry to find them.. but the arcade is vast, and houses tons of single-monster levels and compounds, as well as recipes.

But nothing is too scarce due to 'loot' areas, which provide a bit of everything and so have a very nice payout indeed.