First of all there are no crazy quark charges. This 1/3 is an unphysical scaling factor unknowingly having been introduced when declaring the electron charge the unit charge. This seemed to be reasonable, because no other charge show up in nature than integer multiples of the electron charge. The reason for this is that no free quarks exist in nature. They are bound in neutron and proton hadron quark trinities.
It was only when the existence of quarks was realized that smaller electric charges were found to exist. Relative to the electron charge of -1 they are -1/3 (d) and +2/3 (u). The elctron charge of -1 can be written as -3/3. This shows that the scaling factor of 1/3 is unphysical. the true charges are: electron -3, down quark -1 and up quark +2. All are integer multiples of a unit charge of -1 carried by the d-quark. Defining it as +1 would have been more reasonable.
Now to your 3 2 1 question: The reason is an underlying logical struture, relating electrons and quarks of matter and antimatter. The electron and positron define a minimal frequency bandwidth of minimal energy between -3 an +3 that still allows the incertion of just two additional frequencies - mirrored for matter and antimatter - which do not descructively interfere. The mathematically uniquely possible positions are -1 and +2 (matter) and complementary at +1 and -2 (antimatter).
The logic is a unique solution to a combinatorial problem. It ensures a maximal irregularity in the electric charges of leptons and quarks.It does not only determine the possible number of fundamental particles - one lepton and two quarks (the neutrino is no lepton!) but also determines the frequency relations between these particles. The fascinating aspect of this logic is that it was discovered to exist metaphysically as a mathematical object.
All this will be described in detail in a book on demand,to be released this year