These are the most core mistakes I've seen new players make that come back to haunt them.
- Pause often. Toggling pause is bound to the space bar for a reason: only by pausing liberally will you have the ability to order changes at maximum efficiency. The alternative involves (for example) having crew sitting around doing nothing while waiting for your mouse to get there. (Of course, you could choose to never pause deliberately as a challenge, and the same applies to any other tip on this list.)
- Don't just rush to the next sector - try to explore the current sector as long as you can for opportunities to collect scrap, crew, and so on. If you get caught by the rebel fleet, it's not game over: just tough, fruitless fights until you get to the next sector. (Of course, fighting them several times in a row would be a major setback, so try to keep that to a minimum.) Note that the outer circle of the encroaching rebel fleet indicator is an estimation of where they will be after your jump, not where they currently are.
- Fire your weapons in volleys. This is because shields regenerate rapidly and spreading out several weapons would permit shields to soak far more damage than they should. An exception would be missiles and bombs, which penetrate shields (except the extra Zoltan shield layer) but at the cost of using finite ammunition. Beams, on the other hand, are of no use at all on shields (again, except the extra Zoltan shield layer) and at most will do reduced damage to enemy systems if the beam damage exceeds that of the remaining shields. The goal in inflicting damage becomes to deplete the shields and rapidly follow it up with other attacks.
- While it is tempting to take out the enemy's shields and/or helm first, in order to finish them quicker, a more reliable method of long-term success is to master taking out the means the enemy has to harm you as soon as possible and then continue damaging it often enough that it will not be repaired. This is usually the weapon system, but for some encounters may also include the drones or crew teleporter. Combat is much easier when you're not being forced to react to taking damage perpetually, granting you all the time you need to take out anything else on the enemy ship. Not taking damage also means a saving in scrap you would have spent on repairs, and saving scrap puts you in a better position to win the entire run.
- When in doubt, jump! As long as your engines are powered and your helm is manned, your jump option will eventually gain power and become available, allowing you to abandon combats that are going poorly. Of course, you don't want to overuse this, as you will miss out on opportunities for scrap and such, but some fights are just too costly.
- When a system is knocked out, it becomes depowered. Remember to power up that O2 generator after it has been repaired before everybody suffocates!
These are a little deeper than the bare basics, but still are mostly basic mistakes or things to know:
- Since beam weapons do damage for each room that they cross, experiment with finding ways to align them across the most rooms. As of the release build, even tiny corners of rooms count.
- Drag your most important or longest-charging weapons to the left of the weapon systems palette. As the weapon system takes damage, it prioritizes the remaining energy in the leftmost side. As long as there's still enough power left for those weapons, they will not lose their charge when the weapon system takes damage.
- Consider de-powering your medibay when not in use (which should be the majority of the time). One extra bar of energy goes a long way. Of course, this carries the added difficulty of remembering to power it up again whenever someone gets hurt.
- Upgrading your systems does more than just increase their effectiveness: it also increases their durability. Keep this in mind for otherwise-seemingly-non-critical upgrades such the subsystems (doors, helm, sensors) and the O2 generator.
- If you can route enemy boarders into your powered medbay (for example, by depressurizing the other rooms), you'll have a nice home field advantage in fighting them off.
- Putting out fires with crew members is a whole lot tougher than just depressurizing the rooms the fires are in.
- Don't take depressurizing your O2 generator room, medbay, or door control lightly, because they each introduce a major problem if they become damaged by enemy fire. A depressurized O2 generator room automatically forces your crew to endure suffocation while repairing it. A depressurized medbay may trap you without means of healing the damage from suffocation while you are trying to repair it. A depressurized door control may prevent you from closing doors to allow the oxygenating of rooms in need of repair (including the door control itself).
- If the crew is forced to abandon a repair before it is completed, the current bar being repaired is lost. This can make things extra tricky when dealing with depressurized rooms. This is a situation where a repair drone (which do not require oxygen) could come in handy.
- Don't take removing your pilot from the cockpit lightly. Your dodge chance is a major damage mitigation method, and having no pilot will reduce that to zero or (if you've upgraded the helm) significantly. This also will make it more difficult to escape because it will interrupt your FTL drive charging. Chances are you can spare crew from any other station first.
- Your crew only gains experience for doing things. If you put someone on shield control and never take any shield damage, that crew member won't get experience. Verified by Word of Creator: fighting and repairing only rewards experience on last-hits - the crew member finishing off the enemy or finishing the repair.
The easy and intermediate tips should get you through easy mode in most runs, but once you've mastered those maybe you're looking for ways to do even better! Advanced captaining theory-crafting may well fill a whole forum, however, here's a few tips off the iceberg:
- Instead of immediately spending your scrap on upgrading your ship, try to keep about 100-150 scrap on-hand at all times. This lets you buy the best gear you can find in a store, and can also be a useful nest egg for emergencies such as needing extensive hull repairs or fuel. Of course, you can count what you have to sell towards this total, and you don't want to packrat too much scrap or you're just losing upgrade potency needlessly.
- Learn to visually recognize enemy weapons and how charged they are. This can give you a good idea if your defenses can repel the attack or not.
- You get more scrap for killing the enemy crew than destroying their ship. The typical means to do this is via boarding parties, but with a bit of patience one can also pull this off by bombarding their O2 generator, deliberately targeting their crew with your weapons, or other means. Depending on the situation, this will not always be possible to do, because the enemy ship hull can only take so much abuse.
- If you're experienced enough to know exactly how things are going to go, and feeling like doing some real micromanagement, try swapping out your shield, engine, and oxygen power when you don't need them. As you can imagine, this allows you to deploy a terrifying amount of ordinance and drones against the enemy, but you're in for a world of pain if you guessed wrong.