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.
This is actually an interesting point since people cite this reason for why being good in Fallout 1/2 actually feels good, as you're given plenty of opportunity to be a right bastard. It's also something to point out how the game itself (particularly in the ending) is aware of this and doesn't try to frame it as some complex moral dilemma. Just an action taken by someone who was molded by the "necessary" cruelty of the wasteland.
Still, I'm going to lazily echo someone else here and say the "choice" itself is fine, the consequences however aren't. Destroying one of the only centers of human settlement left in the wasteland for some petty rich fuck should cast a dark shadow on everything else you do, no matter how "good" you are after the fact. Also, Fallout 3 is a much easier game than the first two, so the decision to be evil feels less like selling your soul to save what's left of yourself and more like something arbitrarily cruel, when you can just cruise the game easily as a knight in shining power armor.