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.
Here's my opinion
The choice itself is fine, it's how Bethesda handled it that makes it bad
Tenpenny wanting to nuke Megaton off the face of the Earth because it spoils the view is an excellent example of a petty evil decision
But...
If you nuke Megaton, you don't receive any real consequences from doing it. Your dad being slightly disappointed in you for literally killing one of the only real towns in the Capitol Wasteland isn't a consequence. You don't even lose the biggest quest you get from Megaton (Wasteland Survival Guide) and nobody ever treats you any different.
Hell, you can even get away from the karma hit by giving water to random thirsty people.
It should have been a deliberate, heavy decision on behalf of the game ala becoming a child killer or joining the slavers in Fallout 2, something irredeemable that marks you through the entire game as someone who can't be trusted by decent folk.
Yeah, they should have given you a perk that comes with negatives.
Who's this Tenpenny person? I just blew it up immediately because the crackpot preacher was getting on my nerves.
Guy who owns a tower for rich people at one of the edges of the map and is really bigoted to ghouls.