So, I have maxed all three of the crafters and learned a lot more about crafting, so I have updated the post. I know that a lot of people are confused about the crafters, so I figure I will offer what knowledge I've gained so far.
In Marvel Heroes Omega, there are three crafters and one shop.
The shop, called Quartermaster, is different because he does not require materials, only currency for his transactions. Each slot in his store can only be purchased once. If you see a bundle of three spare parts, you can only purchase it the one time. But, you can press the refresh button and his stock will be renewed. The refresh has 3 charges and each charge has a 30 minute cooldown. Because of this, we will probably be visiting the Quartermaster quite frequently. However, like the crafters he must be leveled up. Increasing his level seems to increase the number of items he offers per refresh. At max he has about 29-31 purchasable slots. Here's the items which Quartermaster offers:
The Engineer is the next crafter. He is important because he can transform some of your materials into the next tier of material. I will create a separate post soon which will cover crafting materials in detail. Basically though, common materials will drop frequently from enemies, but uncommon and rare are much tougher to find as drops, so you will rely on purchasing or crafting these materials. For this reason I recommend maxing EITHER your quartermaster or your engineer first so that you have easy access to these materials.
The Scientist is the replacement for the enchanter from the PC version. She offers really powerful buffs to your equipment for steep fees. "But wait!" I hear you protest, "Gaz said they weren't going to have Uru-forged!" Too true. So here's how it works now:
Enhancements. The scientist can add a buff to one of your items. The buffs she can apply depend on the gear you are enhancing.
She can place modifications on your artifacts. These boosts are pretty potent, though less powerful than the utility armor enhancements. They also require a "Modification Installation Kit." However, they will automatically achieve a max roll as long as the artifact is level 42 or above.
The final crafter is called the Research and Development Analyst. Let's just call her the Analyst. Her job is quite different from the other three. She takes research materials (brown in color) and uses them to craft boxes (called research projects) which grant xp to your other crafters. These projects can also obtain materials and reportedly "rare blueprints." However, in the dev live stream it was confirmed that these rare blueprints are not in the game currently, so I still have no idea what kind of blueprints this would unlock, though I imagine it would include more craftable artifacts. She cannot be donated to and does not have a level. Also, her materials don't seem to drop from normal play. Pretty much you have to purchase them from the Quartermaster.
Use the Analyst to level your crafters!
The Analyst is basically a credit-xp transfer system. The cost of a research material is 400 creds, so the cost of the materials plus the recipe is equal to the amount of crafter xp you will be gaining. So you aren't losing anything by selling your gear and going through the Analyst and you will be gaining some materials and a chance at those "rare blueprints." Once a crafter is max leveled, those research projects are a HUGE rip-off because you aren't getting any crafter xp, so if you want those rare blueprints you are going to be really sacrificing if you didn't just level via the projects.
Visit the Quartermaster to buy research materials constantly!
Here's the issue with the Analyst: the quartermaster will only ever sell you one bundle of each research material per refresh. Thus it will take you a lot of trips to get each project. Also, with the Analyst there is no reason not to work on all three crafters at the same time and if you don't purchase all the research materials you see, you will regret it later.
Equip a Kingpin medallion!
This made crafter leveling very easy for me because every enemy you defeat has a chance to drop a case of money worth 5,000 to donate or sell. The best chance I've seen on a medallion was 5% which worked very well.
Even though I told you to level all your crafters through the Analyst, you are still probably going to be donating because leveling through the Analyst alone will take you a long time. So, I'm going to still offer advice about which crafters to focus on first:
Max either Quartermaster or Engineer first!
You will need the rare materials they offer to use the Scientist who makes the cool stuff. If you are new to the game or aren't confident yet, I think the Engineer should be your first crafter goal. Max him out and use him to craft some super-heroic gear and artifacts before you go try out your super-heroic trial. Alternatively, if you know the game well, you will probably be in super-heroic well before level 60 and would be wasting your time crafting super-heroic gear. The quartermaster offers the same materials, but much more hassle-free, so I think he is just as good a choice to max first.
Max your Scientist second!
The Scientist is the most important crafter, but not until the end-game. Her enhancements are going to be integral to surviving cosmic difficulty, but you probably won't want to use her enhancements until you have cosmic gear that you are quite happy with. Don't be afraid to use her rerolling services a lot. Hopefully we will have data on max stat values soon so that we can make better use of the rerolling recipes, but I wouldn't shy away from it for now.
Let me know if you have any questions or if you spotted something that I am incorrect about. I will make a materials guide soon, so be on the lookout for that.