Why is the definition of the moles as it is?
Here what say The International System of Units (SI)
“Atomic weights” were originally referred to the atomic weight of
oxygen, by general agreement taken as 16. But whereas physicists
separated the isotopes in a mass spectrometer and attributed the
value 16 to one of the isotopes of oxygen, chemists attributed the
same value to the (slightly variable) mixture of isotopes 16, 17 and
18, which was for them the naturally occurring element oxygen.
Finally an agreement between the International Union of Pure and
Applied Physics (IUPAP) and the International Union of Pure and
Applied Chemistry (IUPAC) brought this duality to an end in 1959/60.
Physicists and chemists have ever since agreed to assign the value
12, exactly, to the so-called atomic weight of the isotope of carbon
with mass number 12 (carbon 12, 12C), correctly called the relative
atomic mass Ar( 12C). The unified scale thus obtained gives the
relative atomic and molecular masses, also known as the atomic and
molecular weights, respectively
Atomic Weight' - The Name,
Its History, Definition, And Units
Prepared For Publication By
P. De Bievre' And H. S. Peiser
The unit could be fixed arbitrarily. By choice, it was linked to 12C
and the macroscopic mass unit, the kilogram of the SI. Nevertheless,
one should note from the definition below that the magnitude of that
link factor of NA does not affect the amount of substance of any
entity.
Can we really neglect the mass of electrons when the atoms get bigger?
I would say yes, Neutrons mass is 1.00866491588(49) u for a proton is 1.007276466879(91) u while the electrons at rest have a mass of 0.000548579909 u so even if we take the heaviest atom Oganesson that has 118 electrons we will have as a very approximate weight of the electrons 0.06473242927025999 u.
Why do the element's mass per mole do very rarely end up being integers?
At the root, there is the fact that neither the atomic mass unit u
is an integer actually it's 1.660539040(20)×10−27 kg. The kilogram was defined long before the studies of sub-atomic particles so it wasn't designed to be a perfect multiple of the atomic mass unit. However, even if we decide to adjust the kilogram so that the atomic mass unit is 1.00000000000×10−27 kg we will eventually end up with non-integer masses, this is due mainly to two factors:
Nuclear binding energy
The "mass defect" that is related to the fact that: $$E=mc^{2}$$
So the mass is linked to the energy, different elements have different energy due to different Nuclear binding energy and so different mass!
Neutrons heavier than protons
Neutrons weight 1.00866491588(49) u while protons 1.007276466879(91) u so elements with more protons are heavier.
Isotopic abundance? Not really...
Natural abundance (NA) is not at the root of the problem, your observation is valid not only for Standard atomic weight (Ar, standard,) that take into account the isotopic abundance but also for the weight of single isotopes. The periodic table below shows you that also element without isotopes (blue background) have non integer mass. Of course, if you consider the standard atomic weight of an element ( that is the result of a weighted average so you might already expect that is a non integer... ) the isotopic abundance have a greater impact on the result, but if you consider the atomic mass as defined by IUPAC so you are analyzing a single isotope the root of the problem are the reasons described above.

Holden, N., Coplen, T., Böhlke, J., et al. (2018). IUPAC Periodic
Table of the Elements and Isotopes (IPTEI) for the Education Community
(IUPAC Technical Report). Pure and Applied Chemistry, 90(12), pp.
1833-2092. Retrieved 18 Jan. 2019, from doi:10.1515/pac-2015-0703