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.
I just wish there was a more holistic view taken. A twenty hour story can be fine, but if it's paired with really boring busy work then it drags the experience down.
Well, that's the thing though. "Boring busy work" isn't necessarily and inherently bad. Pathologic 2, for example, is a game that is intentionally miserable to play. A friend of mine calls it a "survival game that's harder than real life." It's a terrible experience, you're practically scrounging in the gutters for pennies you can use to buy bread so you don't starve to death after 12 hours without food.
But it works. It serves a purpose in the game. It's a boring, terrible, miserable gameplay experience but that's a good thing in this case.
That's why games are so difficult to discuss, because things which would be obviously terrible in one game can be done well in other games.
Your example is exactly the kind of holistic view I have in mind. Pathologic's gameplay, story and tone all come together to make an experience like no other.
But there are a lot of games that aren't trying to do that, but which have equally tedious game mechanics paired with a story or tone that don't match them at all. Final Fantasy 7 is about a bunch of punk rebels saving the world, but requires watching numbers go up for twelve hours while the same music loops in your ears over and over again. In that case and in many others, people will ignore the massive dissonance between the story and the gameplay and judge it purely based on what it does well.