...and the best part is all the pieces are sitting right under our noses.
I've had an idea for crafting I've been mulling for a while that I would like to propose. It all started when DStahl let slip the idea of crafting starship a while back. Currently, collected anomalies are used to modify existing items to make them better. When I thought about this in terms of starships, it didn't make any sense. Would you modify an existing ship?
This got me to thinking, about what does go into the construction of a starship? Well, a lot. Let's look at this more simply, what goes into a hand phaser? You have a casing, a power cell, a emitter, a focusing crystal, etc. These are components, still machines, but pieces. If you break the down the components, you get the raw materials, the nuts and bolts so to speak. Bolts, now what does that remind me of? Ah yes, self-sealing stem bolts. Now I'm not saying there are any self-sealing stem bolts in a hand phaser, but I bet you there are a few in your starship. Self-sealing stem bolts are a commodity in STO. Come to think of it, there are a lot of commodities that go into the construction of a starship.
Can you see where I'm going with this? The pieces of a truly robust crafting system are already in the game. STO currently has two systems that are currently languishing, a research system (our current crafting system) and a commodities systems. Combining the two would breath new life into both. All that is needed is a system to bridge the two, a construction system. Let's take a look at how each system would work:
The Commodity system
I see this divided into two categories, raw materials and components. Both can be sold and many can be bought from vendors much like they are now. Raw materials are the simplest commodity. An example would be a Tritanium Sheet. The second type of commodity is a component. While some of the more common components can be purchased from vendors, but the more uncommon ones will have to be created. I'll get more into that later.
Right now, the commodity system is almost ignored. The only time we buy commodities is when we're doing aid the planet missions. Even then, we do them so infrequently that it's usually easier to replicate the commodities instead of looking for the cheapest bargain. If you think, however, of how many tritanium sheets and self-sealing stem bolts go into making a starship, it suddenly becomes a big deal where you can get them for the cheapest.
The Research System
This represents crafting as we now it now. That said, under the new system, it will be applied a little differently. Anomalies are still collected as they always have been. However, instead of using anomalies to improve the phaser as a whole, you use anomalies to modify components and improve them. If you goal is to build a phaser rifle with improved accuracy, your going to need a better targeting scope. While it's possible to manufacture an item without any anomalies, there greatest you'd get is a common item. Anomalies make it more rare.
The Construction System
This is where it all comes together. There are two parts to construction. The first is the manufacturing of components. This involves taking raw materials and producing components from them. Some components can be bought, but if you want the high-grade components necessary for Mark XI equipment, your going to have to make it. Higher grade components will require more expensive materials.
The second part is the final assembly. Once you have all the components necessary to make your phaser, it's time to put it together. The higher the mark of the item, the higher the grade of components required. Some mark levels will share components, so it isn't necessary to have eleven different grades of power cell. A phaser rifle and an energy-dampening armor may both use the same kind of power cell. If you use components that have been modified by research, you increase the rarity of the final item. The researched component used determines what the bonus will be.
So that's my idea in a nutshell. I don't expect something like this to happen quickly, but my hope is that it can leverage two independent systems for the benefit of both and the game as a whole.
What you describe is a ship design system, not a crafting system. Such a system would make more sense as part of the Foundry rather pigeon holed into the crafting system. Keep in mind that ship construction would make up a tiny fraction of crafting.