I have played three chars now and two are @ 50 and one has maxed crafting capability so while I am a bit of a noob and may have missed some vital aspect I feel I have seen the extent of the crafting game now and it strikes me as not having much to contribute in the end game.
Its also quite frustrating though the components of a really nice system exist but they have not been put together right IMHO.
The current system provides cookie cutter crafted items, usually lacking the important additional quality you want and lacking a sense of experimental custom crafted uniqueness which the gameplay could provide.
eg the example which prompted this post is MkV photon torpedos, all that power is useless if they miss, one miss in 10 is like a 10% reduction in DPS so [acc] is key and you can't make photon torpedos more accurate. You can get [acc] photon torpedos from drops but crafting cannot get you one. You can craft [acc] quantum torpedos but not photon.
As a result crafting does not feel like research and design, it feels like a form of expensive mass production or conditional barter.
The crafting system has the potential to be more flexible so you can make items with the unique qualities you want... at a price.
eg The rare particle traces could correspond to and allow certain qualities to be added to crafted items. So adding accuracy for example should require a specialised particle trace or combination of particle traces eg Methogenic and Dekyon for [CrtD] with a plasma torp, maybe just Anyon for adding [acc] to a quantum torp but Anyon and Duderon to add [Acc] for a photon torpedo etc etc... that sort of thing.
The cost of adding the capability (that knowing about that trace allows,) could be where the dilithium cost comes in. Some cost in non replicatable materials should apply to adding the trace and it should scale exponentially with the number of trace related abilities you add. eg 50 , 500, 5000, 50000 etc and if someone wants to add multiple qualities of the same type it should require n+1 rare particle traces with each extra x1 ie 1,2,3,4 so if someone really wants to make an [acc]x5 they can but it will cost 555,550 dilithium and 15 rare particle traces of the same type.
Another aspect of this is that there are several teminals in rooms outside the main R&D area and each terminal is exactly like the R&D in the main room, only without non replicatable materials exchange and bank available. Why ? What a waste! It would be good if each terminal had a specialisation which allowed the adding of particular types of quality to the schematic.
Then you could craft a schematic to your requirements by adding to it at the appropriate terminals in the specialised "laboratories" until it is ready to make and then make the schematic into the finished item with additional costs related to level.
Here's a simple idea to vastly improve crafting: GET RID OF THE DILITHIUM REQUIREMENT.
This is one area in which the desire for income has overstepped its bounds, and needs to be put in check. Without the dilithium, crafting will immediately become somewhat useful again, without changing the items there.
As it stands, though, the dilithium requirements make crafting pointless.
Yeah my fleet has designated crafters simply because of how long it takes to be able to make VA gear. And worse, how much dilithium it costs to rank up your crafting now.
BTW I think that Hargh'Pengs should no longer be BoP. Sure the different factions get them different ways, but ANY player can get one. Feds can play a rather short (and fun!) mission to get one, KDF can get them from a Doff mission, again, essentially free.
There was a thread a while ago where a dev had said that while they were going to look into dilithium costs, there was no way it was going away in crafting. Sucks...
As per the OP, someone in my fleet had a similar idea as yours, choosing what 'bonuses' to add to your stuff. I have a fed character that got to 'master' crafting before F2P, and now I only use her to make Aegis gear for people when they need it. Seems like a waste. I like that idea.
I'd also like to see all marks of purple gear be craftable, as well as being able to craft gear that doesn't drop or isn't purchasable from the DIL store, to make crafting for EC a viable career in this game.
Would be nice, as well, if you could continue to gain crafting SP and get accolades which reduced the amount of unreplicatble parts you needed (to a point, obviously since they won't get rid of them totally) so that people who choose to craft a lot get rewarded and it truly gives meaning to the term 'master craftsman'.