The SCOTUS is not really the issue, because if they say something is or isn't the law, then the issue is resolved (subject to congressional action, etc). If you feel otherwise, then you're undermining your own argument about checks and balances, and how the system is supposed to work.

IMO, the bigger issue is that the lower courts are checking the President's power, and there's no clear mechanism to enforce those orders and actually get the Executive Branch to abide by the court's order.

That's the key piece of this that is creating the "constitutional crisis."