Got lucky, and unlocked a couple of ships quite early : the egi cruiser of course, but also the zoltan adjuducator. I then spent a while just unlocking their layouts. And couldn't get any other ship for days.

Yesterday, unlocked the mantis gila monster (boarding-based runs are a lot of fun), and the federation cruiser. But I "cheated" for the latter : i "saved" my game right at the end and re-did the boss battle a few times, changing tactics and weaponery. So, after that, I reverted to my former profile file, and re-locked the federation cruiser. I'll try this ship when I'll have re-unlocked it fair and square, with no save/reload attempts.

The mantis ships will keep me busy for a while anyway.

Also, I really got it by surprise. Spoiliers make it marginally easier to get these ships, I suppose, by letting you aware of the conditions, but they deprive you of a sudden unexpected ship unlock. Which is a nice moment.

It's uh... special. Like with most unlockables, the upgrade state of each system is awful. The main gimmick gun takes 20 seconds to reload with all the upgrades, and there's no manning it.

Wow, this ship sounds cool. So you suggest, that searching for new ships is better than unlocking B versions?

Actually, not that it's my favorite ship that I've used so far after beating the game the first time my next play through used the osprey and I won again. While having no control over the artillery cannon stinks, the damage it deals saved me more than once (including during the final battl). Unfortunately it cost me several boarding parties because I forgot to disable it. So I wouldn't say it's awful, as I've had more success with it than some other ships.

As far as unlocking ships, I've consistently unlocked them on runs where I at least make it to the last sector. It's been steady for me.

I've taken it as far as unlocking two achievements and trashed it soon afterwards. Then I looked at the B variant. Somehow, it's worse. Maybe it's the 2-person medbay, maybe it's the crappy laser.

I thought the federation cruiser was pretty good. I won the first time I used it, on normal, and absolutely trashed the flagship. With the big gun firing every 20 seconds, combined with the rest of my weapons (may have been lucky there, got two burst lasers and a good missile launcher) it ate through the flagship's armor so quickly I was literally taken by surprise each time the flagship blew up.

Anyway, as for me, I unlocked the Torus quite early. Then, on my 20th game (easy) I won with The Kestrel, unlocking the federation cruiser Osprey. During that run, I also managed to unlock the Bulwark and Nesasio. On my 21th game (normal), I won with the cruiser. No unlocks this time.

The best I've had was Kestrel A with a battery of Burst Mk1, Mk2 and Mk3 and 51% evasion. You wait for the Mk3 to start firing, then pause and manually target the other lasers. That's 10 points of damage delivered in individual packages, ideally taking out the shield first, setting fires and cutting the hull in half with the next burst.

No no. I'm just saying that unlocking layouts is easier and faster. While I was doing this, I didn't stumble upon new ships at all, so these seem more rare and difficult to find. But that's okay for me, I don't look forward to the point where I'll have no "reward" or "achievement" ahead. And I prefer to use one ship to the max (layout A and B) before trying a new one.

So, I'm quite happy with how things turn out so far.

(I still hope for mods and add-on to develop this game in diverse directions, though. But I don't need them for now.)

Those I found were easy.

I got the stealth ship by finding a multipe-planet mission in an Engi system (ie, "hunt down the manthis that stole our schematics").

I got the Zoltan one by picking the right dialog options in a Zoltan sector (he talks to you about peace and then you face a rebel ship, just pick the most peaceful options in the dialog and you'll get it without even having to fight for it).

And of course, you get the Engi ship in sector 5 and the other federation ship by beating the game. Arguably, getting the second federation ship is harder ;). You know, in my opinion, the Kestrel beats the Stealth Ship hands down.

The stealth ship starts without a shield and the Kesnel starts without a cloak.

To get a survivable stealth ship, you'll need both (unless you have insane weapons, but the stealth ship has like 3 weapon slots so good luck with that).

Imo, it's easier to get the former with the later.

Also, the Kesnel has 4 weapon slots (to the stealth's ship 3) and the stealth ship's startup settings are pitiful (no shield & weak guns which means you can't really go for 1 shot stealth kills).

Of course the Kestrel is better than the Stealth Ship, the unlockable ships get unlocked later because they are harder to play, so once you managed the game with the easy ships like kestrel,engi and fed cruiser, you can find new challenges with harder ships. The B Layouts are even more difficult.
So now I can almost always win every normal game with the first 3 ships mentioned above, but I have not managed yet to win with the Stealth Cruiser B Layout. It has no shields and a very slow weapon, meaning even with cloak you always take some hits. And if those hit the weapons bay , you have to repair and wait another 20 secs or so, in other words game over. If the enemy has super shields (that extra green bar), theres not much you can do.Anti-ship drones are trouble too. When those two come together, you;re boned. I'm not sure how to succeed with this one. I am, suspecting the key is to get a second weapon quickly to take out shields before using the glaive.
Engi Ship B seems to be very hard as well, but I only tried once, so far.

Not all unlock-able ships are hard.

The Zoltan Cruiser, Mantis Cruiser and Federation Cruiser are dead easy to play.

The Engi Cruiser is about the same as the Kestral.

Just unlocked the Slug Cruiser. I have a feeling it won't be that hard to play either.

Stealth ship is harder because it relies on strong firepower and starting weapons are average. Also, it has 3 weapon slots & 2 robotic slots so it doesn't have much in terms of offensive capabilities unless you get lucky and find a powerful weapon and it lacks the starting crew to easily become a boarding vessel.

the zoltan cruiser is easy? i have yet to beat the game with it because the layout is crappy and the starting crew sucks at fighting melee.

mantis and slug cruiser are strong because killing the enemy crew nets you more scrap then destroying the ship.

about the stealth cruiser...dont just activate the stealth when is ready. use it do dodge enemy shots by stleathing right after the enemy fired. this makes him waste the shot and stop him from recharing his weapons for some time. getting a shield early is importent, just pray you dont get many enemies with beam weapons.

Dodging the flagships shots this way is awesome but the federation crusier cannot get any stealth. you really need a defense and hull repair drone to survive imo.

engi cruiser is kinda soso because attack drones just dont cut it against the flagships and the mark II drones arent much of an upgrade.

I have won a couple of times with the Stealh Ship A to unlock the other Layout, but Layout B I can't beat, I tried like 20 times and never got past sector 2 or 3. Not sure how to do it.

thats odd, i beat the game with layout b, but not a. granted, i only played them one time each. so it may be luck.
target the enemy weapons first and use the cloak to dodge their shots.