Then when the executive takes more power they have little ability to opposite it. Especially since there is a significant Congressional delegation who believes in the Unitary Executive theory, who will interfere with attempts to rein it in.
I believe it is entirely due to the Founders being intent on pitting Congress against itself, while the President is a single person. They initially tried a half-assed version of that by making the runner up Vice President, but that was quickly seen to be useless.
There is a lot more to be said over a quarter millennium, but that is the fundamental design flaw.