Overhaul the economy and balance out the gameplay in other ways and it's fine.
For example, rad-aways, make them rare, and I mean RARE, then make them cost a lot of caps, say 700caps for one?
Then make doctors be able to heal you for 500 caps.
Might not sound like much but the more things that are tweaked with prices the more caps you'll spend.
There should also be shops that only accept caps, no barter, at all, just caps.
And each shop that do accept trading items should have different values on things, a farmer might spend more caps on water than he will on a weapon.
With the right amount of changes to the economy, trading can be brutal.
But I do not want to be able to "upgrade" towns by spending 20K to their mayor.
I'm all for new things that can help improve the game.
But spending money like this feels like... Fable?
It's an RPG, sadly we'll always get too much money, and even if this thing you suggested was implemented we'd still get too much money after we can't spend any more to upgrade them as they're at their limits.
I disagree with your sentiment that it'd be bad, most wasteland towns you see are dumps because they lack money, if you gave them 20,000 caps, they should be able to fortify the towns walls, increase food imports, or caravan exports, better town protection. I don't think we need to turn towns from small bumbleweed nowhere towns like NoVac into eye-paradises like Vault City, I just think cosmetic differences showing you've made a difference in their lives would be very interesting, if you decide not to help them, they remain status quo. I'm for tweaks, but your whole 'brutal economy' is more fitting for Fallout, back when people were isolated enclaves trying to survive, but now, California, Vegas, and D.C. are on the rise, Chicago might be, and Legion lands are up in the air. Over all, times are changing, I think the prices are fair, there's just nothing to DO with all of that money.