Some items are too rare or overused

Some items are too rare and/or overused. I am not talking endgame items, those should be rare.

Overuse: Items that are in too many formulas - you souldn't have to farm the same enemy for hundreds of a single item

Bovine plume is VERY overused. It is needed for a large number of upgrades related to movement (High Jump, Accelerator, etc.), but drops from one enemy that appears in only 2 locations in the Oriental Sorcery Lab. This makes farming it to the levels you need very boring. Although at least one of the Haagenti is near the travel room. It would be better if there was more variety in upgrade items, or at least if more enemies had them. It's not fun spending an hour and a half killing the same mob over and over. And I love how they feel the need to single it out  for removal in NG+, because so much depends on this one item that having it early can actually break the game.

Flight Feather is not as overused as Bovine Plume, but it's still overused, and drill only drops from one enemy, the Ocypete, in  the back end of the Cathedral. They are more common than the Haagenti, But it would still be nice if the farming location wasn't so restricted.

Same for Witch's Tear, although at least this can be farmed simultaneously with the Flight Feather by running between the hallway and bell chamber above the chapel.

These three seem to be needed for most major shard upgrades.

Too Rare: Mostly these items are only in chests, but are used far beyond the available level (usually 2 per blue chest reset), to the point where farming them becomes about getting blue chests to reset

Soy Sauce only comes from chests in the Oriental Sorcery Lab. Note chests, not enemies, so you can only get around 2 per trip to the lab. With the number of recipes it is in, it needs to be more common, or at least drop from enemies so you can more effectively farm it.

Black pepper has the same problem as soy sauce. You are constantly trying to get the max 2 per visit to the Underground Sorcery Lab, even though it's in a lot of recipes. Put it on an enemy so you can farm it.

Because I know it will be brought up, my complaint here is not about difficulty, It's about boredom. Revisiting areas can be fun, but farming things that only comes from chests or single enemies that are only in one or two places is boring, because you are doing the exact same thing in the exact same place for hours. I'm not saying make it easy (if i wanted that, I would talk about the drop rate on orichalcum), I'm saying make it less repetitive.