With a limited amount of credits and/or rins at your disposal, how does a pilgrim decide which one to upgrade? Here are some tips.
Early in the game, it's often the most best choice to focus on getting good armor first. The reasoning behind this:
That's not even considering all the backtracking that players might have to go through to get their armor repaired. This can cost quite a bit of time and valuable fuel. Flying back and forth eats up fuel, because it requires the thrusters to be fire. Floating around waiting for the ship's shields to recharge, however, does not. Players can also go longer without repairs if their armor is better. It increases a pilot's effective combat range and reduces dependency on stations. Keep in mind that “higher level” doesn't always mean “better”… if that expensive, specialized armor cannot be repaired without backtracking two systems, that will kill the flow of the game pretty effectively. Also stressful: trying to repair a critically damaged segment of the ship's armor plating right in the middle of combat. This sort of scenario usually involves scrolling frantically through a list of twenty items, many of them identical-looking, to find an armor repair barrel/patch/kit and use it before the ship's hull is breached by enemy fire.
While it may be tempting to go for the most powerful shield available, it's actually a good idea to pick shields that trade in all those fancy resistances for reduced power consumption. These shields, of which Deflectors are a good example, regenerate slowly; nonetheless, they can soak up more damage to your ship's armor than a lower-level shield. Main use: diving into combat and quickly killing the most dangerous enemies. The wise pilgrim tries to acquire a higher-level shield with as much HP as he/she can, for as little power-use as possible. Level IV shields will take less damage than level I-III shields, apart from any other defensive abilities – simply because their level is higher.
From St. Katherine's Star onwards, though, the player will pretty much be forced to switch to power-hungry shields. In these cases, look for the fastest shield regeneration instead of large amounts of HP. Players who habitually clear out the most dangerous enemies (as soon as they gate into a new system) can cruise around without shields active… most of the time( disable the shield using the “B” key in-game). In these low-intensity combat zones, regenerating armor, a patcher arm or a patch spider really help out. A good strategy is to stick with an equipment set that can repair itself automatically for as long as is possible, relying more on power-slurping but decent shield in the mid-game. It saves on retreating, repairing and refueling.
When the player finally does encounter that special shield that they think will see you through the mid-part of their game, they can use a ShieldEfficiency cube on it to knock down its power use by 20%. Algorithm cubes require an installed HeisenMachines quantum computer to be used. It's best to use the efficiency cube before the pilgrim gets access to Domina's "Ingenuity" power… because it selects a random device to enhance, she might increase the shield's HP instead of its efficiency. But more HP doesn't mean squat when you can't spare the power to use it.
It's also possible to enhance a reactor's power output, increasing the available power for firing stonger weapons; before players (normally) get access to their Domina powers, ship reactors can be enhanced by the University in the large orbital arcology in St. Katherine's Star, and pretty cheaply as well. If players refrain from upgrading their reactor straight away, waiting until they find a better one… well, they could suddenly find yourself with power to spare.
Protip: make sure that weapons and devices not currently in use are disabled. An X-ray laser that is installed, but not used because more powerful particle weapons are available, it's still using 10% of its normal power. Add the drain from that laser collimator that's probably still installed and that starts adding up fast. When additional protection is sorely needed, switch the shield generator back on the ship is quickly fully shielded again. In this scenario, 10HP regen on a 80HP shield is better than 3HP regen on a 200HP shield.
Good defensive equipment in the “vanilla” (unmodified) game:
There's some more stuff, but these are the big ones.