Why are electrons taken implicitly to be the elementary charge? It would save a lot of fractions in particle physics problems.
It's a matter of history. When George Stoney developed Stoney units in 1881, or when Robert Millikan performed the oil drop experiment in 1909, it wasn't yet known that it was possible for anything to have a charge smaller in magnitude than the charge of an electron. By the time the quark model was proposed, in 1964, the use of the "elementary charge" being taken to be the magnitude of the charge of an electron was already firmly established. Changing the definition of an "elementary charge" unit due to the quark having been discovered would have led to too much confusion.