I hate agreeing with people who can't get "their" brain around "there", "they're" and "their" skip 1st grade? but yes, like almost everything in STO since PWE, the crafting system is now totally insane and broken. if I didn't have a lifetime account, I would have stopped playing like all but 5 of my 200+ friends. PWE is killing STO. that is a fact.
I actually sat down and did the math - with the exception of Starship Weapons which run at a touch under 71% of the Dilithium Store's prices in terms of Dilithium (really effing expensive, but still cheaper than the store) everything else that requires unreplicatable materials has a dilithium cost that is about 60% of what you'd pay to get the equivalent item in the D-Store.
And this is without doing your crafting during a "Time to Craft" event where the prices fall to 57% for Starship Weapons, and 48% for everything else.
Is it expensive yes? Is it broken? Not as completely as most people argue. I honestly feel like crafting, especially high end crafting is only broken because you can't obtain unreplicatable materials in any other way than the current one which requires you to spend dilithium. At present it's primary value is to give access to the Aegis Set and consoles. You can craft Blue Mk XI consoles for less than 8,000 refined dilithium at any time and even less than that during a "Time to Craft" event. For some consoles it is cheaper in terms of effort and currency to get them off the exchange, on others it is by far cheaper to get it by crafting.
For you guys that quoted exchange prices, you obviously don't get that part of crafting is hunting down the materials yourself. Unless you're trying to outfit your entire ground crew in one go you can usually find the data samples you need with about an hour's worth of exploration missions in the appropriate star cluster. Incidentally only the orange data samples used to craft the Aegis set don't have a star cluster where they are the only find (on the Fed Side that is). Probably not a coincidence.