Okay, so while I like the current crafting system, there are a lot of ways to improve the current system.
One way, is to remove the store listing. Instead, you turn in anomalous data to Romaine, or whomever. And she'll say, "Hmm, very interesting..." or something along those lines, something technobabbly. Then, she may ask for, a common shield, or weapon, or something, and boom, you get your green item back. In addition, each time you repeat a recipe(since you can't see it), vary whats needed a bit randomly, make it somewhat unpredictable. In addition, slowly, if you grind a recipe many times, the resource costs should go down.
Then, as you unlock the next tier(include a notification!), the same process happens, but more specialized. Each researcher will say, "Oh, I'd like to see some mutagenic particles" for example, to help guide the players.
Finally, when you are Commander rank(or have a Commander rank BO), you can help "study" the data, and based on your skills, abilities, career, you can create items unique to what your build is.