These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
That One Disadvantage: Besides the game making you a One-Hit-Point Wonder, if you lose a companion, and choose to not recruit another one, you're doing this trope on purpose. Some companions has a few disadvantages, which can make you easier to get killed or cornered: Naomi can't doing anything, besides serving as a radar (until later), Ivanoff and Kamiya can stun the monster, but lacks Naomi's radar (and the latter locks you into a bad ending), and Rene has limited stuns, and the same disadvantage as Ivanoff and Kamiya.
Scrappy Mechanic: The "Auto Map". It fills out the area you're in as you explorer it but doors doesn't appear on it. Sometimes you even have to walk up against a wall for it to "map" it.
Varying on your experience with the game, many mechanics in the game:
The companion mechanic: With one, you can survive a hit, but you lose said companion.
Keeping Naomi alive: Makes the whole game a No Damage Run. Given her radar ability, it shouldn't be too hard, but screw up once, and you'll need to save scum.
Getting new companions: If you lose one, very far away from the town-hub, you'll have to navigate the gameworld without getting hit once, find the available companion of your choice, and continue.
Fridge Horror: Be chased through the underground by cultists and a monster, just to find out that you are the reason behind not only the train wreckage, but also the kidnappings that have been going on. And why? Because you are the Dark Messiah. Finding out that multiple people have been kidnapped, and finding out your a monster, must be horrible.