The fundamental problem is that political parties (and, in particular, a two-party system) render the existing constitutional checks and balances useless. As long as you have political parties with members spanning all three branches, they are not truly separate branches.

We lived in the illusion that this wasn't the case for nearly 250 years because most of the time, elected officials have largely acted in good faith. However, the Republican party (correctly) determined that when it comes to wielding power most effectively, it's in their best interest to protect its own members in all branches rather than members in each branch thinking of themselves as independent of (or even in conflict with) the other two branches as the constitution envisions.