Keep in mind that, even in Trek, there are SOME things you can't replicate.
That's stuff that can be added to some sort of mercantile system later on, but it ought to be secondary in Trek, since it's secondary on the shows. By the time we get Ferengi as a faction it would be grand.
Wow, great ideas here. Sorry that your post got hijacked by folks wanting to talk about updating Mem. Alpha 'crafting'. While that is all well and good your ideas compliment an updating Mem Alpha system, not compete with it.
Cryptic would do well to take these ideas under advisement.
OP has an interesting idea. It has some flaws that would need to be worked out, but I'll leave that to everyone else (& the dev team) to point out/worry about. My input is, beyond "crafting" items or feats/skills/etc, this would be an excellent opportunity to introduce something a lot of people here have been wanting: Role Playing Content. "Crafting" could be used to generate a series of RPG related elements that doesn't necessarily benefit you in any particular situation. For instance, my character could learn "Art" and then "Craft" pictures, perhaps some how through an altered screenshot option that would allow me to share it. Another character could "Craft: Musican" (or something similar to this) and play an exotic instrument like the Vulcan lute. Other examples that I'll allow your imagination to expand on include:
You can imagine a number of different special skills and abilities these "Crafts" or "Professions" might gain access to. Please feel free to add to the list, or expand ideas as you see fit. Note: Some of these kind of sit on top of each other, like Entertainer and Dancer. Dancer could be a sub-choice of Entertainer, and other choices in Entertainer could include Magician, Musician (which would have its own subcategory), Actor, HoloStar, etc.
Weightlifting: Extra melee physical damage. Precedent: Big dudes like Worf. Each rank increases physical damage by 1%.
Warp core engineering: Actually faster warp speed travel time in sector space. Precedent: Tom Paris, Warp 10. Geordi: Any number of extended 9.8+ trips. Each rank 1-50 increases warp travel speed by 1%.
Equipment enhancements: various small abilities on your gear. 1-10: tricorder ground scans leave visible waypoint on nearby targets for 10 seconds. 11-20: Basic weapon cooldown, -0.4 seconds, and so on. Precedent: Wesley and others are always tinkering with and enhancing stuff.
Stellar cartography: Ability to find anomalies in Exploration areas at a greater range of 2% per rank.
Track and field: increase your sprint speed by 1% for each rank.
Diplomacy (once we have diplomacy missions, which are coming): 1% more likely to succeed/get favorable response per rank.
Tribble breeding: increase tribble spawn time by 1% per rank.
Terrestrial forensics: 0.5% increased likelihood of causing a loot spawn on the ground per rank on each kill.
Spatial forensics: 0.5% increased likelihood of causing a loot spawn on in space per rank on each kill.
Commerce: 0.5% increased sales price of all gear sold to non-replicator vendors per rank, and 0.5% reduced cost of purchase from all non-replicator vendors per rank.
Replicator efficiency: 1% reduced replicator cost on purchases per rank.
It just occurred to me that if Cryptic said they would do something like this, and if it was just numbers/text in-game (all it would need to be, really), and asked for people to suggest in a thread skills along these lines, we could easily get hundreds of possibilities (hell, you could do hundreds just cribbing off the Memory Alpha site without getting into "real life" skills). With say 10 skills per player character and say 3 per BOFF, you could have absolutely unique characters and crews.