Well after seeing all of the matrix movies more times than is healty, I have discovered that you can do an actual equation that explains many things about the conflict throughout the trilogy. It also definitively explains why Neo and Smith were destroyed. It is not perfect, but what I have discovered so far is as follows:
Lets call neo X.
In revolutions, the Oracle says that smith is neo's "Negative".
So, lets call smith -X.
But, as you see throughout the series, Smith is not less powerful than neo as -X and X would imply. He is actually equal in strength, you must change it to
Now we must factor in the Oracle and Architect's effect on the equation that they so often mentioned.
The Oracle (O we will say) does and has always aided the resistance, and in turn, Neo, so we must add her to X as she "unbalances the equation".
|X|+O is not equal to |-X|
And so we have an unbalanced equation, but as we all know, the architect is there to balance it out. He aids the continued control of humans, and in turn, Smith. Also, since he is the father of the matrix and she is the mother, 0=A.
So, now we have the balanced equation
That is the equation going into the super burly brawl. After an impressive demonstration of their equality, Smith imprints himself onto Neo, thus "adding" himself to neo. Now, we can solve the equation.
Thats it. Zero. They canceled each other out. This explains why they both were destroyed and Neo is, in fact, dead.