@katiekats It is really, really hard to make a game that has natural difficulty that remains challenging without being intentionally obtuse.  It requires a lot of game design acumen that most game designers just don't have, so they take shortcuts.  A few shortcuts are to be expected - the mark of good design is knowing which corners to cut - but start cutting stuff down too much, and people notice.

And FTL is NOT challenging normally, so they have to devise means to make it challenging through artifical means, and it shows.  Not only in the final boss fight, although its REALLY NOTICABLE there, but also in the encounters like you describe.