Simple answer is that the devs want crafted items to be inferior to loot drops. The most likely reason for that is because its easier to manage. If the best gear was craftable at a reasonable price, then people would craft stuff more often (duh) and then flood the exchange with it. Prices on that gear would bottom out and nobody could sell any loot drops because that loot would not be as good.
While I think this is definitely true, I think it's also possible to fix, with a bit of creativity and no real systems changes.
More unique gear that is only from crafting like how we have the Aegis set. Make the crafting gear a little cheaper because it is expensive needing Schematics + Data Samples/Particle Traces (boring way to acquire) + Unreplicateable Materials (costs Dilithium to buy). That is just wrong wrong wrong costing requirements to craft stuff.
There are lots of ways to make it more involved and immersive. Its just not that kind of a game though. Everything is pretty much simple mode, they are appealing to Star Trek fan base which is older and has day jobs. Skill gain is quick, combat is point and click, no item loss on death, consumables can be replicated instead of bought from vendors, etc. No room for complex resource gathering systems, crafting skill trees, all that jazz, its not that kind of game.
Crafting is so bad because just about everything in it is worthless. If you're going to pay stupid quantities of minerals for something, it had better be top of the line, or there's no use. Why bother buying stuff you're just going to flush down the terlet anyway? So much of it is bound, so the resale value is nil. It fails to alter the end result, other than that you wind up poorer for it.
If it was free junk you could assemble with other free junk, it would have a purpose. If it was GOOD stuff, it would have a purpose. But paying stupid quantities of minerals for vendortrash? Forget it. Just more worthless garbage like most of the junk in the D-Store, a button that no longer serves any useful purpose other than a trick for scamming newbies who don't realize how worthless that stuff is.