Ok, Here's the things I thought about and the current conclusion I've got.
Possiblity 1: Time based constraints. Current. Crap
Possibility 2: Traditional crafting constrained by access to specific materials. Pros: retrains crafting in a realistic fashion. Cons: Requires each item to have a list of components, a lot of book keeping and limited custom utility. Meh.
Possibility 3: Single item crafting. The idea that each project needs one specific rare item to be done. Pros: restrains crafting without requiring as much bookkeeping or fiddly searching. More simple than classic crafting. Cons: Effectively just a level of abstraction; if one item is all thats needed than really why not just find the object itself as loot because thats effectively what you've done. Its like a voucher for your gun or armor or whatever. Not to mention it also means that we run into the thing where I'll have to start doling out these specific items in specific ways to keep things balanced. Also has limited custom utility.
Possibility 4: Builder tickets: You can make whatever instantly so long as you're on the ship and meet certain requirements, but you can only make so many things in a single time period. Pros: It would work, maybe. Cons: Completely artificial and thus annoying and bullshit. Could say it represented time or whatever but then things get increasingly abstract. Also it becomes builder foodstamps and I don't like being that guy handing out cans of value brand weapons on the government dime.
Possibility 5: Tag system: So I got this idea thinking back about the test we did a while back with perplexicon as objects. Specifically rather than basing crafting on specific item recipes, I base it on specific tags and give these tags to items. For example, lets say you want to make a gun, a pistol specifically. The pistol has a recipe of
Pistol: Structure 3, Blast 1, Projectile 1
That means you need a material with the tag of "Structure" at quality 3, a material with Blast quality 1 and material that is projectile 1 as well.
Structure would be found on just about anything that is solid enough to build out of. Wood, metal, bone, brick, stone, etc. Stronger materials have higher quality.
Blast would be on things that burn or explode, higher quality, bigger boom.
Projectile would be on anything that can be used as a projectile, from ball bearings to pebbles to darts. Better quality would mean bigger damage.
So basically what we would have is a big list of tags and I would look at an item and say "That looks like it needs these tags of this quality" and crafters could try to find literally anything that fit those tags (or higher) and use those things. No recipe calling for the specific snot of some critter that you may never find. Instead we may end up with lots of weird but interesting stuff like people carving pistols out of whale bones and using bullets made of fire elemental blood and golem eyeballs.
But hey, thats pretty neat.