You're not fleeing a rebel armada hellbent on destroying you, you are mining maps for scrap. Think of it like a business in the random encounter harvesting industry. The worst maps points are the ones that will cost you scrap. That means avoid tough fights. Run away when you see that they have the worst possible combination of systems/weapons. Sometimes this can be relatively wimpy ships that just happen to have your number for whatever reason.
For most non-stealth ships, upgrading to shields 2 by the beginning of map 2 can make a huge difference in mitigating scrap loss to nickling and diming from every encounter.
Increase your odds of getting positive blue choice encounters by maintaining a diverse crew and upgrading medbay, sensors, piloting and doors to at least level 2 early on.
Cloning negates a lot of crew-killing random choice events.
When you spot a store on the map, earn as much as you can ahead of the rebel wave before hopping in to see what items they have.
Mercenary delays are almost always worth it, but sometimes an early map scouting is better.
Boarding and suffocating earn the best loot.
Even when you know the game inside out, expect to lose 2/3.
The hacking module is insanely versatile and a great gap-filler/countermeasure when you really get the hang of all the nasty things you can do with.
The first Engi stealth cruiser is pretty easy to get and IMO probably the most well-rounded ship in the game once you get your stealth game down. Starting out with LR scanners negates its only weakness, asteroid fields.
Non-asteroid-field hazards are usually best avoided, even when you have a powerful build, pulsars in particular.
Avoid lengthy recharge super-weapons early on unless you have cloak. You need good D for those or you'll take too many hits before you can use them. Burst 2s are very nice early-game finds and quite nasty in multiples for the energy cost. Shield reducers + beams are the duh combo.
Don't use missiles/drones if you can get through the fight without taking a hit without them.
Pay close attention to Zoltan shielded ship systems before engaging, especially if you rely on teleport or bombs.
Augment, system and weapon combos that are amazing:
* Long range scanner - So cheap, loads of blue choice events and the next best thing to an early map reveal
* Weapon pre-igniter and anything that can get past their defenses - Always be on the lookout for one of these.
* Defense scrambler and missiles, drones, and the hacking module in particular - seriously if you spot a defense scrambler it's probably worth grabbing even if you don't have hack, drones or missiles yet. Also, hull missiles hurt if you target empty rooms.
* Cloaking, hacking module, beams - beams don't cancel cloak, hacking at 2 cancels shields up to 3. This with double glaive beams will one-shot the final boss but don't kill yourself trying to score two glaives or one too early.
* Reconstructive Teleport, cloning, teleport
* Drone Recovery arm, drones/hacking module - drones are pricey
* Any boarding build and mind control and/or hacking module
* Hell, hacking + mind control alone are downright nasty. Very easy to suffocate.
* Zoltan bypass and bombs - Zoltan shields + a nasty system combo can really ruin your day unless you have this
* A crystal crew member and teleporter