There seem to be only a very few fundamental forces governing all aspects of the observable universe. I think that when we understand what those forces are and how they operate all the complex issues that develop from those forces will become simple. Newton had three laws that described motion on earth pretty well. Mathematics is based on a few basic postulates. Both motion and mathematics can become very complex when extrapolated to the nth degree, but the basic arguments are very simple.
You noted that "The best available theories of the universe ... are in fundamental disagreement as to the fundamental constitution of the universe". This is undisputably so. Could it be that the problem is with the popular misunderstanding of one of the fundamental forces? I think so, and I believe I know exactly what caused this misunderstanding.
In The Principia, Isaac Newton often used the word attraction to describe "the centrepitency, or propension of the whole body towards the center" (The Principia by Isaac Newton translated by Andrew Motte: Definition VIII). And even though Newton dedicated an entire paragraph (the last in the definition) to explaining that when he used the term attraction he did not mean a physical property, almost everyone has assumed that attraction is the physical property he was describing. Even though the man himself said it was not so.
So, I think that if science would revisit the concept of gravity, what it is and how it works, it could rectify many of the seeming contradictions that flow from a flawed understanding of one of the fundamental forces of nature. And this is why I say that the universe is not that complicated.