This whole situation really goes to show that both the judiciary and the legislature need to be greatly expanded -- probably by 10 fold or more. Even if you greatly reduce the size of the federal government.
The executive employs approximately 3,000,000 employees. The federal judiciary only employs about 30,000 total, and the legislature about 20,000 total. The sheer velocity with which the executive can ram through questionable directives *and have them executed upon* (despite the law) means the other "co-equal" branches of government are always potentially on the back foot. It's just a personnel game. Trump has only highlighted how absurdly easy it is to abuse this imbalance.
And after the Chevron and Trump decisions, it's only going to get worse and worse. I do think these Federalist Society types who pushed these unitary executive theory ideas have now created a monster. They've created a situation where the executive has immunity to simply apply the law however it wants, clogging up the judiciary with civil and federal suits, and where the Congress cannot pass laws fast enough or with great enough specificity to avoid defying Chevron or avoid executive misapplication. Meanwhile the executive has long since moved on from the original issue to the next 10 issues, and the next 10, and the next 10, while the courts and the Congress are still only getting started on the first few problems. And the executive will never really get "punished" for these actions because of its supposed immunity.
And presidential elections don't really help with this problem. Because one president has 4 years to drastically reshape everything, and the next president will spend all of their 4 years reverting it, dropping all the previous suits, creating its own litany of new suits, and rinse and repeat. The hysteresis of this process is too long and leads to instability and chaos.
What about Chevron is a problem in this particular case, though? My understanding is that ditching the doctrine of Chevron deference puts more power back in the hands of the judiciary.