Why do we still call the electron charge the elementary (EM) charge? The electron is an elementary particle, part of the SM, pointlike, with no substructure, or spatial extent. Its intrinsic properties include its EM charge, which we still call the elementary charge.
Originally the name electron comes from electric ion, and it was discovered around the 1900s.
Though we still call it (the electron's Em charge) the elementary charge.
Since we call it the elementary charge, it was believed that every single object in the universe had a EM charge that was larger (multiples) then the elementary charge, and the elementary charge of the electron was indivisible.
The elementary charge is a fundamental physical constant.

Charge quantization is the principle that the charge of any object is an integer multiple of the elementary charge. Thus, an object's charge can be exactly 0 e, or exactly 1 e, −1 e, 2 e, etc., but not, say, 
  (1/2)e, or −3.8 e, etc.
  This is the reason for the terminology "elementary charge": it is meant to imply that it is an indivisible unit of charge.

https://en.wikipedia.org/wiki/Elementary_charge
Now in 1964, we discovered the down quark, with EM charge of one third of the electron. Since then, the elementary EM charge should be that of the down quark, and the electron should have three times the elementary EM charge (of the down quark).
Now I believe that the true elementary EM charge is the down quark and its EM charge should be the fundamental physical constant.
I do understand that quarks are in confinement and have never been observed outside confinement experimentally, but still I believe that the down quark charge is the real indivisible elementary EM charge.
Question:


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*Why do we still call the electron the elementary EM charge and why is the -e still the fundamental physical constant (and not the down quark)?

 A: Lets start with the basic definitions:

The elementary charge, usually denoted by e or sometimes $q_e$, is the electric charge carried by a single proton or, equivalently, the magnitude of the electric charge carried by a single electron, which has charge −1 e

Charge is a quantity measured in the laboratory, and in coulombs, 
is $1.60217662 × 10^{-19}$ coulombs.
What is a Coulomb?

The coulomb (symbol: C) is the International System of Units (SI) unit of electric charge. It is the charge (symbol: Q or q) transported by a constant current of one ampere in one second.

It is obvious why the proton charge  was called elementary, compared with the coulomb, the charges measured at the time that protons were formulated. It is also based on the understanding of the periodic table of elements , and it was logical for people studying chemistry and nuclear physics to give the definition of elementary, instead of carrying multiples of $1.60217662 × 10^{-19}$ coulombs : define it as 1 and carry on with a simpler symbolic life.
Then quarks and  the standard model came up, and the model fits the data with some charges being 2/3 and 1/3 of the definition for the charge of the proton.
You ask:

Why do we still call the electron the elementary EM charge and why is the -e still the fundamental physical constant (and not the down quark)?

(Note it is the proton too involved in the definition of elementary charge).
Because mainly, as people said in comments, one does not have individual quarks to be able to measure their charge to the  accuracy of $1.60217662 × 10^{-19}$ coulombs, and standard units should be based on accurate measurements, which can only be carried out with protons and electrons.
If in the far future it is found experimentally that the onion has still many layers of compositeness, would one want to change units to those of the theoretical particles in  the new models?
The value of the charge of the protons and electrons does not need elaborate mathematical  models  to be measured in the lab, only classical electrodynamics and mechanics.
Of course there have always been philosophically  inclined physicists,  believing in the reality of the ideals of Plato, that mathematics creates reality, and in this frame the mathematics of the standard model creates reality for them. But for realists, as is the committee that defines the System of Units, measurements are of greater import. They still have the Coulomb as a unit of charge.
