Whenever you have a chief executive at the top of any organization, that individual will have an inordinate amount of power. And people will say you need a tightly run ship to get anything done.
But during the Revolutionary War, we had the Continental Congress running things. They had a presiding officer to keep the floor in order, but mostly the Congress acted as a committee of the whole when making major decisions and somehow we won the war. And after the war the Congress was doing okay, even if it was a little chaotic. They somehow passed the Northwest Ordinance to settle the land West of the Appalachian mountains. The economy was a little tough. Each state had to have operating taxes to keep running, which they mostly got from import and export taxes, so interstate commerce was chaotic , but it was okay. But the system wasn't stable enough for business speculators, like John Hancock, Robert Morris, Alexander Hamilton, and George Washington. They needed a strong executive government so they could make the big money, which brought us the Constitution.
There might be three branches of government, but the executive is the only one set up to do anything. Congress will sit there and argue and debate and even when they pass something that looks good, there is so much legalese and loopholes that it is worthless. The whole process is more or less to let people blow off steam because the executive is going to prevail in the end.
The process is why I stopped going to church. The church council would make a decision on some policy, but the the pastor and the moneyed people in the congregation would just do what they wanted. And same in a corporation. They'd have these team meetings where it seemed like everyone was getting to put in their input, but in the end the boss rules.
What Trump is doing now is just shortening the process. Every president has had his way, from Jefferson buying the Louisiana Purchase to Ollie North running Black Ops out of the basement of the Reagan White House. But they usually let Congress and the country blow off a little steam. Trump is saying, I haven't got time for that as you people never do anything anyway, so I'll just do what I want.
Congress, theoretically, could withhold funds, but there are no funds. Things are just paid for with IOUs. The only thing to stop him is our military or some coalition of other countries.
The only permanent solution is to get rid of this centralized executive form of government and go back to a chaotic but de-centralized congressional government.