This new system is even worse. At some point, the Judiciary will make a poor ruling. Perhaps this ruling is impossible to hold to, but maybe the executive branch decides to usurp the court of its own volition. Then what?
The checks and balances system of our government only works when everyone plays nice. But if push comes to shove, then the executive branch is the one that holds all the power. They don't have to obey the legislator nor the judiciary -- neither has any real capability to enforce their will.
The country has been slow rolling into single pillar government structure for decades now. IMHO, this ruling is a huge step towards solidifying the executive branch as the de facto sole branch of government. Government agencies were provided a mechanism for all three branches of government to work together, legislators provided scope and leadership, the judiciary provided checks, and the executive provided the operations.
Once the agencies are all gutted, a future administration is going get an opportunity to act on their own via executive authority and they will ignore any attempts by the court to stop them, because the court is literally powerless in all but word. And that's what opens the door to a president who begins seizing assets of political opponents.
Lots of authoritarian countries masquerade as democracies because legislators and judiciaries are inherently powerless to stop executives.
I know plenty of people will counter with the old way was supporting an authoritarian executive. But to them, I'll point out that the agency system has ~100 years of efficacy behind it.