Wow, clearly a motherload-inspired game, but a great leap over all the other imitators! The mild platforming mechanics are an excellent addition, and I love the unobtrusive humor (for example, the wireless wires and their explanation).
I have suggestions that you could have implemented, without much extra work, that would have improved the game even further (imho).
1. the refueling and repair animations are excellent (as are all the others), but it takes too long. Repair and refueling should be instantaneous when you enter the ship.
2. Add a "back" (or "up") option in the crafting screens. For example, crafting item 1 requires item 2, which requires item 3. After you craft item 3, you click "back" and it returns you to item 2. After crafting item 2, you click "back" which then returns you to item 1. Also, you need an option to allow you to "split" bigger items, but from within the menu for the smaller item that you will be creating more of.
3. Color for the minerals and metals in your inventory. This would make them much easier to differentiate by eye. This isn't necessary for the artifacts and more complicated parts since they are easier to tell apart (although it would look MUCH nicer). The gameplay itself is so bright and colorful, which makes the monotone graphics in the menus seem very very dull and out of place.
4. The research logs should appear in order. This isn't System Shock - these are your character's own records! Also, I was initially really confused at how the logs appeared to bear absolutely no relation to the identity of the artifact - it is really not apparent at first that even though they are identified by name in the research screen, your character doesn't know what they are. So you've got this important part of the story-telling BACKWARDS: your character knows what happened to him/it, but this information is hidden from the player, whereas the player knows what these items are but doesn't realize that this information is hidden from the character! You should have removed the names from the artifacts, and then had an early log entry make the unknown nature of these "artifacts" clearer.
5. The integrated youtube videos are an interesting idea, even if they're not exactly necessary as implemented here. But you need a way to speed the appearance of the written text - many of us can and do read faster than the narrator speaks.
Finally, the ending was a real letdown (the main reason for the half-star off) - you select the special planet...and are merely treated to another text-only "video". Yes, most players probably won't even get that far, but you could have done SOMETHING to reward your more dedicated players besides hinting at a sequel. An extra-deep planet with something to find at the bottom would have worked.