No; you're attempting to evade the central point by changing the argument to a typical Republican/Democratic slugfest.
I don't care about the merits of Congressional prerogatives here, which is an entirely secondary point. The point is that the Founding Fathers believed that Congress would defend its own prerogatives against the executive. This has been proven false: a model where government is dominated by partisan prerogatives is far more descriptive of reality than one where branches-of-governments pursue their own prerogatives.
Your latter point--that a Republican Congress investigated and obstructed a Democratic President--is true, but it is, again, an indication that Congress is driven by the needs of the political parties who happen to be running it at the time, not as an institution in itself.
This is entirely contrary to what the vaunted Founding Fathers intended or expected. Not least because the main thinkers among them thought the system would prevent the development of political parties. The Constitution was theorized to deal with abstractions that don't correspond to reality, and it doesn't even consider the most important driver of politics and governance not only in the contemporary world but in the world that existed a year after it was ratified.
In a world where political parties are accepted as a given and inevitable, no one would write anything like the Constitution and expect it to be effective. And no one has: even after WW2, when the US was drafting constitutions for its defeated opponents, it went with documents entirely unlike our own.