[Shujin]

"Neat, I found this Rockdirt Shuriken that's sharp, but oh, I guess it's trash because it's not Rockdirt +5."

Yeah, I can see why this might not be wanted. I was simply thinking that this would be a way to get people more interacting with each other. The higher Level material wouldn´t be findable in dungeons.
And with science you can always have the chance to upgrade that weapon you find to a higher material Level, aslong as you get the recipe.

But yeah I agree to the rest aswell. The "Trash" materials could also just get a little buff.

though I'm slightly worried it may trivialize certain things like Qwarence's Breakdown Shop.

Not so sure about this, since you can basically breakdown everything with the portable science kit wherever you want anyway. Sure it´s a donation item, but I don´t think it will really trivialize that shop more than this.
I mean not everyone will level up science anyway. And in my opinion players who want to go in the "Shop owner" direction, should get an advantage over NPC at some point.

If anything had to be overhauled, I'd say it should be Metalworking, Tailoring and Woodworking. Metalworking is very useful while Woodworking is okay at best and Tailoring is very lacking.

Agreed aswell. Was just tossing in ideas.

Oh, yeah and addition of Lightning material please xD