YES!

[dyno101]

Nearly 500 runs.
7 ships. All layouts for each.
Crystal B. Pike beam, S-bomb.
2 crystal, 2 mantis.
I beat stage 1 of the rebel flagship.
Tried stage 2. You don't truly know what a power surge is until you're hit by it.
Died to it in less than a minute.
BUT finally making that sort of progress warmed me up.

[stylesrj]

500 runs and you haven't beaten the Flagship?
Just how much is the RNG screwing you over, especially when you're flying the Crystal Best?

[Fireclaw27]

I don't really like the crystal ships, and find them hard to play. I love crystal boarding, but I only seem to get AI ships, trying to warn the fleet, too close too a sun, when I play as Crystal B. I don't know about A, but I find B to be a pretty hard ship. I mean, it's OK, but definitely not the best ship. That title goes to the shrike.
(By the way, considering what people say about Crystal B, I'm probably playing it wrong. If you know how to do it properly, please tell me)

[stylesrj]

If you encounter too many AI ships or Zoltan-shielded ships in Sector 1, restart. Not worth just holding out for FTL with no rewards and hull damage for your troubles.

As for how to use Crystal B when the stars are aligned just right? Send the first two guys in, lock down the Weapons and slaughter the enemy within. If you need more time to disable the guns, use the second guy's lockdown and bring the third one in. Evasion won't be needed if the enemy can't fight back. Also, you have a cloak. 150 Scrap saved!

Then, hope for someone not a Crystal or Mantis or Rock or Zoltan to replace the pilot, hope to get some guns and then go play the Lanius Best.

[dyno101]

500 runs and you haven't beaten the Flagship?
Just how much is the RNG screwing you over, especially when you're flying the Crystal Best?

A lot.
I had 2 crystals and 2 mantis as my boarding party, which is pretty darned murderous.
Take out the shields, and love that I got a pike beam.
But power surges are just... death. Pure, molten-hot death.
And you can't disable them, no matter how broken their drone system is.
I would've dusted my hands and won if I had survived the first power surge, seeing as the flagship's zoltan shield would be gone fast because of the length of the pike beam.
And a death blossom vs. 4 shields isn't that damaging, seeing as a max of 3 bullets can hit me. (If my facts are straight.)
But, the RNG must've been generous for me to get the crystal cruiser (All the sectors needed, perfectly in row...).
It's probably because all of my strategies are based around getting ships. I'm not the kind of players who always sets their sights meticulously on winning. I even got the Fed cruiser through its quest.

[stylesrj]

The Power Surge shouldn't be something to worry about when you have a crew of murder-monsters.

Disable the missiles in every stage, keep the triple laser crew alive (be sure to murder the others though) and use your cloak during a surge.

Stage 3 also has a Power Surge but it's a lot easier to avoid as you can cloak for a second to avoid everything, then fire everything in return to get your cloak down and charging up again for the next one. But I do recommend ion weapons and something to counter mind control... or a Clone Bay if you can't avoid your crew turning on each other.

[dyno101]

The Power Surge shouldn't be something to worry about when you have a crew of murder-monsters.

Disable the missiles in every stage, keep the triple laser crew alive (be sure to murder the others though) and use your cloak during a surge.

Stage 3 also has a Power Surge but it's a lot easier to avoid as you can cloak for a second to avoid everything, then fire everything in return to get your cloak down and charging up again for the next one. But I do recommend ion weapons and something to counter mind control... or a Clone Bay if you can't avoid your crew turning on each other.

Oh yeah..
I forgot that I had cloak.
...
And that's why I haven't beaten FTL yet.

[stylesrj]

I tend to forget about cloak as soon as I buy it.

I get so used to flying without it that when the Breach Missile slams into my Cloaking device, I'm like "Oh yeah! I actually had a cloak I could have used!"

[dyno101]

PROGRESS UPDATE!
Last night, I beat the rebel flagship's second stage.
I used a strategy that involves making the Fed A really tanky and relying on its artillery beam.
I had a Burst MK 2 and a Flak 1.
So I think all I need to do is make that Flak 1 a Flak 2 and it'll be a winning ship.
I had my artillery beam maxed, and plan to do so for this next strategy.
I'll also see if I can get my hands on some ion weapons, since that'll just make it a lot easier.

[stylesrj]

And yet Stage 3 somehow wasn't even easier?

Also, Fed A? Back before AE I could never beat the Flagship with that ship