The choice of blowing up or saving Megaton in Fallout 3 is often cited as an example of bad game design, but it's actually just fine. It is usually criticized for being not morally complex enough, being just a choice between being good or being evil for next to no reason, but this assumes the only role of a moral choice in games is to offer the player a neat little morality puzzle to solve.
Let's, for argument's sake, imagine an alternative FO3 from a parallel universe, where instead of it being a choice, it was just a normal quest of you saving a town from exploding. Maybe the guy even shows up to tell you to blow it up instead, but there is no way to actually do it. Wouldn't the experience of saving Megaton be lesser in this game?
Being able to destroy Megaton makes you saving it feel more meaningful, as a moral good only exists in relation to a moral evil, and making the choice real makes the game better.
It's still a pretty shit game otherwise, though.
It honestly really depends. Games are a very diverse medium, and it's possible for gameplay and writing to matter in varying amounts depending on what the game is. I don't play Tetris or Geometry Wars expecting a story of any kind, let alone a well written one. And I don't play visual novels expecting to have a deep level of control over my actions.
But when I play an RPG which is ostensibly about player choice and expression, I don't care as much about the gameplay, but expect that I will be able to make meaningful choices within the story- not necessarily in the sense of choosing an ending or choosing a faction, but there should be a way to roleplay as something other than the bestest boy or the worst piece of shit who ever lived. I expect that the player character has some agency- again, maybe they don't do so in such a way that everything hinges on them, but I expect them to do more as a character than "look for my dad and then do that thing my dad was gonna do, and then let this other NPC lead the fight in the end while I'm just there"