This is why the movie was so far reaching in scope. The question itself of
the various matrixes we exist under. I think a synonym to matrix would be
'illusions'. So the question might be better simplified and understood as a
question, 'What illusions do we exist under today'? And there would be
many; perhaps all of it.
Of course, the first to come to mind would be the Christ illusion as C3
correctly alludes to I think. But what about the very enculturated values
we are born into? I mean, why "IS" murder wrong for instance? Why 'should'
we wear clothes? The question of marriage has become such a tender issue
these days, but why "any' marriage at all? On and on, we find the illusive
qualities of a kind of 'cyber-space' reality we exist under, not of computer
machines, but of the organic computer atop our heads that has succinctly
ascribed to imprinted worlds based upon our experience with it over time.
The more we move our existence under the visage of science, the more we
withdraw from our 'matrix' worlds that have evolved through simple
experience, and we take on more and more the characterization of the
machine...cold, logical, rational, barren...much like the barren wasteland
where Zion existed in the movie.
There is no easy answer as to 'should' we take the blue pill or the red
pill. Most rationalists would look upon old world traditions as ignorant
backwardness...much as the awakened citizens of Zion would have seen the
still asleep members of the matrix as fodder for the stronger scourge of the
machines [or whatever mesmerizing evil domain that might exist].
I might be said [by those rationalists], that anything that keeps us away
from reality is a tyranny that should be resisted: Knowledge and
enlightenment at all costs. Yet, life when it comes right down to it
remains just a 'subjective experience' no matter what matrix we might happen
to exist under, even that of the scientific machine. So, perhaps even that
we might have a choice between the blue or red pill, could be just another
illusion...just another box within a bigger box...just another matrix to
resolve consciousness upon.
If so, then it may be the deeper understanding, the more keen intelligence,
the wiser mode of operation...to be able to not try and escape our matrixes,
but only to CHOOSE within which one to exist.
This is why I have personally chosen Christianity BTW. I feel it offers the
greatest hope, the richer experiences, and the greater rewards for the short
time we are conscious. I base this upon the aspect of this thing we call
love...something the movie also understood as a fulcrum upon which choices
are ultimately made. But beware the charelton snake oil charmers. Every
single matrix has them.