I just can't play FTL. I don't think it's a great game. It's average to good. It's more a success for crowd-funding rather than the return of roguelikes into the modern gaming lexicon. It's too random, and not in the same way that Roguelikes are random. It's more about finding the Golden Run (or getting lucky enough to have one) than overcoming the random challenges presented on generation of the game. It's more like it forces you to fight that random uberbeast you'd find upon occasion and instead of being able to run from it, you're forced to fight it. If you run it just makes you weaker for the next fight.
The unstable equilibrium of the game is just way too much for me, and, like you said, the Flagship pretty much requires a few select builds per ship layouts to beat. It pretty much runs anathema to the concepts the rest of the game ran on. That's worse than the randomness. It's basically one giant luck-based mission, and the developers are just fine with that.