Eh, I don't know that I disagree with this. Literally the first character you meet on your way into Megaton is a water beggar who will tell you how scarce water is in, and how they have water inside the city walls but for a steep price. And the fact that Megaton has water, but the purifier is on the pritz and threatening to break down, actually re-enforces the theme, that access to water is extremely fragile.
Don't misunderstand me here: While I disagree that Megaton
contradicts the main plot, I think both of the two aspects were very poorly handled. The Water Beggars outside of the settlements are one of the only things in the setting that establishes the scarcity of water, and there are only like 3 of them. THere's also a couple of ghouls fighting over a fridge in one random encounter, but that's it. It's very easy to totally miss that the main conflict of the game is over water, people don't talk about it and it doesn't influence many things.
And the purifier storyline in Megaton is bad for the reasons you list. Why doesn't anyone care about the purifier other than Walter? Why isn't Walter rich? What authority is Walter under, why is he just supplying this municipality with water? The purifier is just taken as a given without any sense of how it's there or how it's really run. It exists purely to give a side objective that has something to do with water, without doing any of the legwork to actually build out the world and think through the relationships within it.
Pic related, New Reno's jail