Stealth Ship A -- "The Nesasio"
Pros:
*Starts with 4 points in Engines
*Starts with 2 points in Sensors
*Starts with Titanium System Casing
*Starts with Long Range Scanners
*Dual Lasers provide 2 1-damage shots for 1 power
*Great for avoiding environmental dangers and other beacon hazards
*Great for scouting beacon types for quests/stores
*Good against Automated Ships and non-beam weaponed ships early on
*Looks sleek
Cons:
*No starting shields
*While Dual Lasers and Mini-beam are effective for the power usage, they are rather weak after sector 1
*Can be expensive to maintain -- no early shields means frequent hull damage.
*Vulnerable to ships with drones
*Fires can be hazardous because of tricky bay door placement
*Hard to face Zoltan ships early on, because of lack of firepower
*If cloaks are damaged, can mean heavy damage for your ship
*Only 3 weapon slots
Stealth Ship B -- "DA-SR 12"
Pros:
*Starts with the Glaive Beam, a high-level beam weapon
*Starts with 2 points in Sensors
*Starts with Long Range Scanners
*Starts with Zoltan Crew member
*Starts with 2 points in Cloaks
*Powerful against ships with 2 shields or less
Cons:
*Sacrifices points in engines to power the Glaive Beam
*Lacks Titanium System Casing
*Med Bay has only 2 spots
*Glaive Beam takes a long time to spool; ship is vulnerable early on
*Glaive Beam is the only starting weapon
*Without extra power in weapons, Glaive Beam is easily disabled early on
*Only 3 weapon slots
Now, that's quite a list of Cons for both ships, but despite that, and with some patience, I guarantee that you can use the Stealth Ship effectively. I beat the game my first time on normal using the Nesasio.
Here are my tips:
1. MOST IMPORTANT OF ALL -- LEARN TO USE YOUR CLOAK. You shouldn't just use your cloak to stop weapon locks. To be fully effective, you need to time when you turn it on. With the exception of ships with drones, you should be able to fight all ships in Sectors 1 and 2 without much difficulty. Do not cloak immediately when you see your enemy, UNLESS you're fighting drones or Zoltan ships. Wait until just after they fire their lasers or missiles, and then turn it on. This will boost your evasion significantly, and the weapons will harmlessly whiz by your ship 7-9 times out of 10.
This is vital if you're flying the Stealth Ship B. Because the Glaive Beam takes time to charge, you don't want to waste that first 10 seconds of ceasefire. Unless you're fighting drones or ships with beam weapons, you should be safe until they fire their first salvo. Cloak right when they fire their first salvo and your cloak (if it's a least level 2) should buy you just enough time to fire your beam.
Also, your cloak stops weapons locks. But if you wait and cloak RIGHT before they fire, they'll just fire upon you immediately after your cloak wears off. If you cloak AFTER they fire, not only do they waste a salvo on you, but their weapons don't even start charging until your cloak wears off.
2. Obviously, level cloaks as soon as possible. There are only 3 levels and it only costs 50 scrap to level it up from level 2 to level 3.
3. It's going to take a little luck to get on your feet. You'll do well in Sector 1 as long as you don't encounter too many Zoltan ships or ships with drones.
4. Time your dual laser to fire right before your mini-beam. The mini-beam is instant, so you need to use your dual laser to drop their shields BEFORE you draw the beam on their ship. But don't wait too long or the shields will pop back up.
5. I always target weapons systems first with my dual laser and then draw a beam over the weapons and shields simultaneously, if possible. Since you have no shields, your priority is disabling their weapons.
6. Try to use your cloak to effectively avoid damage, so that you save scrap. My first major investment is always a shield. Even level 1 shields will take you far; combined with your level 3 cloaking, you will be hard to hit.
7. You only have 3 weapons slots, but you can still do damage. When I won, I had a Burst Laster III, a Breach Bomb II, and an Ion Bomb II. I would Ion Bomb the Shields, Burst Laster the Weapons, and use my Breach Bomb to prevent further threats if I needed to.
8. The Stealth Ship B is actually very powerful. If you cloak effectively, you can get through the first two sectors with ease. I made it to Sector 3 with minimal hull damage and expenses. But upgrade your weapons as soon as you can. Even a level 1 missile will buttress your Glaive Beam significantly.
9. A Teleporter is a great addition to Stealth Ship A, but isn't as good on Stealth Ship B because of the small Med-Bay.
10. Invest in drones later in the game. Even the Defense Drone I goes a long way to keep missiles off your tail. I had a Defense Drone II when I beat the game.
11. This is a great ship to use if you're trying to unlock ships. Because of the Long Range Scanner, you can streamline your journey so that you hit those Distress Beacons if you're trying to unlock the secret ship. It's also great for the Slug Ship quest, because you can see which beacons have ships in them and maximize your chances to complete that quest.
12. Titanium Casing is -not- a shit Augmentation. When you're fighting and a missile hits your cloaking and you see that, although it still did hull damage, it did not do systems damage, you'll be grateful that you had the little boost.
13. Try to hit as many rooms as possible with your beam rooms. You can easily cover 3 with the mini-beam, and 4 with the Glaive Beam. You only have to have a pixel-esque part of the line in the room to register.
14. Be mindful of your cloak charging time. Always pause after a battle to let it charge -- or it will still be charging when you fight your next battle. Also, if you finish a fight while cloaked and leave, you will start the next fight cloaked.
I'll have more tips on the way later, but this should get you well on your way to playing effectively with the Stealth Ships. I will answer specific questions with later posts.