It is not a flaw but a choice made by the GOP.
Unfortunately turns out that in practice two of the three don't actually have any power at all when push comes to shove.
Congress does not have an army they can send out to enforce any law they pass, so turns out the president can simply just ignore it all without consequences. What are they going to do?
Exactly, that's the bug. Two of the three branches of government can only write sternly worded opinions on paper. Only one has the brute force to impose their will. So there really is only one branch of government in the US.
There's no democratic system of government that's completely immune to a majority of voters actively trying to erode and damage the system.