I'll not get into the details of WHY the current crafting system is "Bad", suffice to say it just is. However I have come up with an idea to "Fix" the system using already in game items and mechanics.
Currently when you complete exploration missions you get Exploration Badges, Rank 1 - 5.
Currently when you scan anomolies you get "Data" that appears to be tieared in roughly 5 tiers.
You can currently "Trade In" your Exploration Badges for gear
You can currently "Trade In' Data in random amounts with items to "Upgrade" said items.
So why not do the following:
Data sample sets translate directly into X amount of Exploration Badges.
For example 1 Each of the Tier 1 data would equal 10 Rank 1 Exploration Badges.
MOVE the exploration badge vendors to Memory Alpha
Convert the existing Data upgraders at Memory Alpha to be Exploration Badge upgraders.
Treat "Updgrades" as a "Slot" on an items, which appears to be what your currently doing anyway.. Green is 1 Slot, Blue is 2 Slot, Purple is 3 slot..
Break the "Upgrades" up into different types and have them require differing amounts of Rank 1 to 5 badges. For instance if I wanted to Add "Efficient" to a Combat Hyper Drive, have it cost me 2 Rank badges for each MK (1-10) of the Drive. An Example would be a MK 1 drive would require just 2 Rank 1 Exploration Badges to add "Efficient", however a MK X Drive would require 2 Rank 1, 2, 3 4, and 5 Exploration Badges. (Note that DOES seem extremetly cheap, not suggesting you use that price but you GET the concept)
What converting to this system would fix:
Useless Rank X Exploration badges once you outlevel them. Personally I'm sitting on 150 Rank 1 badges, a bunch of Rank 2, and some Rank 3 that have no use to me as a captain.
Data sample "Out Growing" and or the Need for exhorbitant amounts of sample farming.
Ties together two seemingly related systems that inexplicably currently DONT work together! (I mean shouldn't I be getting exploration credit for finding "data" ? It just makes sense)