Executive appointees are not unilateral, they have to be approved by the legislature. And setting aside appointments, you also have politicized budget appropri

Executive appointees are not unilateral, they have to be approved by the legislature. And setting aside appointments, you also have politicized budget appropriations, i.e. how can you be certain that the government will adequately fund an agency if there exists a large enough contingent devoted to gutting it? Either you're suggesting creating an agency whose appointments have no accountability from the legislature, or whose budget has no accountability from the legislature. If that's not what you're suggesting, then the core problem is not the system of government itself, it's the polity, the people who are actually voting for that government. You can't have an effective government if half the governed don't want to be a part of that government with you.