Quantum theory is only "controversial" to the general public, mainly because we haven't found a way to explain in simple terms things like superposition, entanglement, quantum tunneling. Quantum theory is spectacularly successful, though incomplete.
Even the "simple" stuff like the uncertainty principle takes a detailed understanding to properly grasp why there are pairs of properties that are inherently linked, and that information about one dictates how much you can know about the other. e.g. position/momentum and energy/time.