Yeah, if I understand, the original idea of the checks & balances in the US was that each branch of government would be fighting to become the most powerful and so they all had ways to stop each other. But it wasn't really designed to deal with the idea that political parties would grow in power enough to supersede the branches of government as the top-level entities fighting for power.
This idea that you'd be able to form a large enough coalition across Congress, the Supreme Court and the Presidency that you could get all three branches to work together wasn't really considered back then. With more localized politics that was basically impossible and so the individual branches were fighting for power.
Our form of government should be updated to reflect the reality of more powerful political parties.