Some modules can be completely re-written for better results, for instance our tax system could be replaced by some type of flat-tax.
Other ones can get by with significant refactoring over a long period, maybe financial regulation could have better consumer protection and ultimately allow for a more equitable distribution of wealth (I'm' not economist, maybe those goals don't even involve each other)
And other ones just need bug patches, for instance interstate commerce, which I'd guess is smooth as a cucumber right now, but we could have more states align on issues of policy that create confusion in the marketplace (a Delaware C copr is a great example of people finding those simple solutions).
It is hard to think of a really good, functioning part of government, but generally those are the ones we don't even notice. The government is great at handing out money to people, and that is often touted as the only social program we really need. We can reform the broken way it hands out contracts to companies.
Here's the thing. Starting over is a fanciful idea, but completely stupid. When you re-build a system, you have to re-build the parts that worked too. And for what it's worth, democracy works and change happens. Yes it sucks that it's slow, but it's sure.