The problem isn't so much that you need to throw sand in the gears. We've eroded some of the checks there used to be (e.g. moving to US Senators having statewide elections instead of being elected by state legislatures) and maybe we should put them back, but in general the system of checks and balances works kind of okay.
The issue is that it's not perfect, and it's never going to be perfect, so you're occasionally going to have things get past the gauntlet and make it into law when they shouldn't. And over time those things accumulate.
So what you need is a functioning process for clearing out the cruft even once it's already there. Something like, make it much easier to repeal rules than enact them.