I think the root of the problem is our two party system and the polarization of our culture. Congress and the president often act as a single partisan unit, not a collection of independent thinkers with their own ideas about how the country should be run. That makes it very hard for congress to serve as an effective check on presidential powers.

That's really the achilles heel of a checks and balances system. Should an ideology gain control of all of them then the system doesn't work and it immediately sinks into authoritarianism. The Supreme Court acting on this just unfortunately gives the illusion of things working when it's a game of blitzkrieg. Make an obvious illegal action and get as much done as possible then when you are eventually checked, move on to the next thing. Just keep pushing in different directions until you cover the board.