Although the system seems complicated, and leaves much in the way for
Bureaucracy to mess up, you must first understand where the
Framers were coming from, what their mindset was when creating this system.
The problem is Power. According to John Locke's Social Contract, the people give their consent to the government to safeguard their natural rights. Therefore, you want a government strong enough to set things right and enforce laws.
The downside to this is that power is bad. If you give it to a person, it will turn them into a dictator eventually. Absolute Power Corrupts Absolutely. Committees don't work, just read George Orwell's Animal Farm, as they begin to share the power only among themselves and not work in the public's best interest.
The government needs to have this power to function, but it's too dangerous to center anywhere, too dangerous for one to wield. The Lord of the Rings is an allegory of this symbolic power.
How to handle it? The Framers decided to spread it out. By stretching it among three branches, it's designed to give the government the necessary power, but it's stretched so thin, it's like a gossamer spiderweb. A single politician can't make any changes, but a team of them working together will bring about results.
Power is so dangerous that they spread it to these three branches. One branch can't be corrupted by the greed for power, and will be cut down to size by the other two branches. Each branch is monitored by the others, to keep stability.
The president can't just gain power, take it all away and hurt the citizens. Congress wouldn't support any of it, and the president is mostly powerless if the Congress is not on his side.
There have been cases where the checks and balances nearly failed, such as the impeachment of Andrew Johnson, the Line-item veto. George W. Bush came close by appointing cabinet members without consent of congress.