I agree with you 97%. Basic science is going through "crisis of understanding", "crisis of representation and interpretation." Cause: The basis of physics and mathematics, the basis of all fundamental knowledge is built on the "home-brewed philosophy."
Fundamental knowledge, mathematics and physics, requires a deep ontological justification (basification). In fundamental physics is necessary to introduce an ontological standard justification (basification) along with the empirical standard.
Rabindranath Tagore gave a good hint mathematicians and physicists:
I ask my destiny - what power is this
That cruelly drives me onward without rest?
My destiny says, "Look round!"
I turn back and see It is
I myself that is ever pushing me from behind.
I invite you to see my analysis of the philosophical foundations of mathematics and physics, the method of ontological constructing a new basis of unified knowledge - the primordial generating structure, "La Structure mère" as the ontological framework, carcass and foundation of knowledge, the core of which - the ontological (structural, cosmic) memory. I believe that the scientific picture of the world should be the same rich senses of the "LifeWorld» (E.Husserl), as a picture of the world lyricists , poets and philosophers.
Is now needed a great synthesis of knowledge accumulated by mankind, including traditional to go to the comprehensive paradigm of overcome "the crisis of understanding", especially in mathematics and physics.