Checks and balances as a concept of governance has existed since ancient Greece and the Roman republic. In a system of checks and balances, also known as the "separation of powers," government is divided into several semiautonomous branches. While the idea of separating powers is not particularly controversial, the extent to which it is implemented is.
Prevents Tyranny of Minority
The central concept behind checks and balances, even in antiquity, was preventing a small group or a single individual from seizing and monopolising power. By separating power into distinct branches, for example, legislative, executive and judicial, each with a distinct interest in maintaining its stake in the political process, tyranny of a minority group is stymied -- within a liberal democracy, that is.
Prevents Tyranny of Majority
Checks and balances resolves the problem of a majority imposing tyrannical laws or imposing unreasonable laws that negatively impact the minority. James Madison, principal author of the U.S. Constitution, asserted that the U.S. did not need a tyranny of the majority: "If a majority be united by a common interest, the rights of the minority will be insecure." Other Founding Fathers held similar beliefs.
Inherent in the Constitution is the notion that competing factions will essentially self-annihilate in terms of abuse of power. Each party in the minority position will seek to shift the balance of power by bringing the corrupt practices of the ruling party to light. In this way, competition between self-interested actors essentially self-regulates the power structure.
Slows Governing Process
The biggest drawback of checks and balances is that it slows the governing process. Division of power usually entails cooperation and compromise between competing factions and this can, depending on the level of political polarisation, significantly slow the legislative process. Whereas, in a fusion of powers system, a ruling party can draft legislation and wield executive power simultaneously, a single opposing branch in a checks and balances system can hold up the entire governing process.