For those struggling and getting frustrated, here's our winning strategy.

[AuRus]

Starting off, if you enjoy the challenge, don't read this. I've played 4 games so far with my brother, we lost the first on mild because we had no idea what was going on, but after that we breezed through the next 3 games and have now beaten all difficulties first try.We are both veteran deckbuilder players and we quickly figured out how to optimize each role. Our strategy each time has come down to this for the higher difficulties.

Pilot: Focus on draw more cards and card destruction, this isn't too hard since you get first pick when resupplying. This significantly decreases the chances of missing a resupply on a turn. Late game start picking up silks and hunt the rare ingredient. Be VERY careful if you're behind on crisis events, you can get one shot by the event that instantly resolves them all for 4 damage each if you have 4. Also note that the time forward events EFFECT LIFE SUPPORT, so don't fly into the unknown if life support is damage (stick to spots you asked around about for resupplies)

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Cook: You are the most important character on the team. Early game your goal is to gain the following cards: 2 reshufflers, 1-2 diplomobots, 1 shield restore (optional), grab a couple ingredients early so you're sure to be able to afford them. The reshufflers are by far the most important, once you get 2 you will effectively be cycling through almost your entire deck every turn. Don't worry about the win condition until your team has become op. Pay close attention to who does not have critical cards (engineer repair, pilot engage, sci research if other two are good) and use flambes / free samples to get them more chances at them. Mid to late game you should be aiming to resolve every crisis with diplomobot.

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Scientist: This is my usual upgrade path (Prioritize buying energy cards always)
Early:
Pilot: Nothing
Cook: 2 flambe or free sample, recommend using foresight with 4-5 points at some point to avoid the rest
Sci: Ignore, maybe mutate you foresight after you get them on your engineer. If you have too few points for your priorities, blind research yourself as everything is useful.
Engineer: Mutate his upgrades so they can be played for free, also try to get 2 wrench/duct tape on him, he's the best to blind research as all but one of his upgrades are good early (exterminate tends to get wasted.

Mid game:
Pilot: Search for 1 Backtrack and one Overdrive, then continue to neglect forever.
Cook: Get the remaining flambe's/free samples
Sci: Get yourself both breakthroughs and a fast track
Engineer: Everything

Late Game:
Whatever you can afford, though the pilot doesn't need anything. Once you get all your required stuff start giving your strong silks to the pilot as you are useless.

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Engineer: Pretty straightforward. Repair all the broken junk and avoid taking any more than one food item (Energy is all you need) The cook should be helping keep your deck size down, but if you have spare cards move and dump them on your cook unless you need it to buy a non-leftovers. Upgrade shields to 4, then ftl to 3, then max shields. Prioritize draw and power cards, though the scientist will be giving you all the cards you actually need.

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General:
-Don't forget your sci/pilot are expendable early game, sometimes it's better to give your money to the cook/engineer and then grab a leftovers so they can afford powerful cards (especially the cook)
-Events that make you discard cards are brutal to your turn, unless you're taking hull damage it might be better to just take the hit so you aren't forced to get leftovers.
-Never, ever take your pilot out of his room early game. It's not worth the risk of the door event locking you out of the cockpit even though it's a small chance.
-Everything is less important that your engineer having a wrench/duct tape in his hand. Throw your powergloves (Literally give him the card) or unomas draws toward him if your desperate. There is a very high chance of hull damage if he can't fix you up early.
-Remember that your engineer is the last to buy, make sure he has something useful to buy as he's pretty important.

[chaney]

Generally some decent advice, thanks for the nice write up.

I'll let players seek out their own methods, but wanted to voice a major strategy disagreement on some Science, in particular the Engineer. I rarely (never) give the Engineer any of his Science cards except the third Wrench (which I identify as a high priority with Foresight) and, if his Artificial Ingredient is required, of course he gets that when needed. The lure of the Duct Tape is compelling, but I skip those, too. They are another card that, while giving 3 repair, may prevent you from having a wrench that can repair a lot more than 3. By late game, I target to have the Engineer to have a deck of no more than 15 cards, 10 is better. Lots of Power Gloves, "enough" Toasters (1-2) so he can self-prune whatever he can, the wrenches, and 1-2 good Sylk (or possibly his Quantum power instead if you have enough trashing to get it down to that.) Keep it small, toasting Refined Sylk if you have to, but toast something every turn.

I also like to get The Captain both Overdrive cards (awesome) and probably nothing else. Backtrack is conditionally useful, and of course a required Artificial Ingredient can't be skipped, but don't bother with it if it isn't needed for a recipe.

The Cook gets both Flambe as a first priority, and POSSIBLY one Free Sample or Discard Dive, depending on the game situation. The cook has enough self trashing (Taste Test) that it's not too dangerous to do some blind Science for him, but don't let it get out of hand, he should be taking cards from other characters to trash instead.