Maybe the proton is not complex but the process to probe it is. Proton is an aggregate of emergent phenomena like mass and its resultant properties. For a simplistic model assume that proton is a tetrahedron with energy wave generators at the vertices and how those waves interact with each other creates the emergent phenomena like mass, charge etc. It will be difficult to probe such a tetrahedron by just studying the properties of the waves and the peaks in those waves/interference which are perceived as particles by the probes.