It helps to have a vague plan, or sense of how your ship build should go. You can't plan specific weapons or equipment, but you can plan for upgrades. You can also know in advance how much firepower you will need by a certain sector, and as that sector approaches, focus more on obtaining it.
My basic plan is for a "normal" ship (one based primarily on weapons and shields) is:
Secor 1: Save 50 scrap. Immediatly upon obtaining 50 scrap, upgrade to L2 shields. Then save to upgrade the reactor until you no longer need to power down O2 to power all shields, engines, and weapons. Skip stores unless you are desperate for repairs because you don't have enough spare scrap to buy anything.
Sector 2: Can my ship's weapons hurt a ship with 2 shields? If not my primary objective is to obtain a weapon that can. Come sector 3 all enemies will have 2 shields so we need to prepare for this. Secondary objective is drone control for missile defence. If I have lots of scrap but can't find drone control I will sometimes purchase a teleporter here (depending on crew) or upgrade engines.
Sectors 3 and 4: We need to start planning now to be able to take on ships with 3 shields. A few enemies may have 3 shields in sector 4, but come sector 5, most enemies will. Make sure to keep 100 or so scrap in the bank so if you see a weapon that will boost you to 3 shield killing power you can buy it. If you don't have drone control yet, try to reserve enough scrap for a weapon and drone control. Other objectives by the end of sector 4 are L4 engines and L3 shields. Ideally, I go into sector 5 able to hurt 3 shield ships, 3 shields on my ship, L4 engines, and a defence drone.
Sector 5: First priority is to meet whichever goals from sector 4 I haven't met yet

. There is usually at least one of these. Next, it's time to come up with an end game strategy. I evaluate my build and determine what i need to compliment it with. If I need more things from stores I aggressively look for stores. If not, I just collect as much scrap as possible. I always try to plan in sector 5 how I will take down ships with 4 shields which will show up in sector 7, and it is not too early to start thinking about the Boss. The plan should incorporate as much current equipment as possible, as refitting the entire ship is very risky and expensive. Work with what you have.
Sector 6: I try to realize the build I planned in sector 5. Shop if necessary, else just farm scrap. Prioritize dealing with enemies with 4 shields over boss fighting, as ships in sector 7 will have 4 shields. I also try to get 4 shields on my ship sometime in sector 6 or 7.
Sector 7: Now it's time to seriously think about the Boss fight. Plan for each phase seperatly if you have to. For instance, a Fire Bomb is great in phase 1 for helping to kill crew, but an Ion Bomb is much better in phase 3 for taking down the Zoltan shield. I often switch weapons between Boss phases. If I don't have 4 shields yet, that is a high priority.
Last Stand: Fighting here is dangerous. If you don't think you can take the Boss you will usually have trouble with the other ships in this sector too. Unless you are really desperate, just go straight to the Boss incorporating as many Repair systems in your path as possible to boost your stores of missiles and drones. This is not the time to take risks. This is the time to execute your plan against a known foe.
A few other tips:
(1) Long Range Scanners. Buy it if you see it. It is the best 30 scrap you will ever spend. Let's you avoid hazards and reduces wasted jumps. I consider all other Augments just luxury, but I will make compremises to my overall game plan to get the Scanners.
(2) If you use drones for offense, a Drone Recovery Arm is essential.
(3) Play with other ships to familiarize yourself with other weapons/strategies. Learn how to use every available weapon so you know how to use whatever you find. Play the Engi A ship to learn how to use Ions and Drones. Play the Mantis ship to learn how to use the teleporter. Play Stealth A to learn how to use the cloak.