The pilots are chosen from a pool of children whose mothers have died, the reason for this is due to the requirements for a specific person to pilot a specific Eva-unit. They are said to contain the souls of the pilot's mother. With the exception of the clone, Rei.
Using the 2003 PlayStation video game as a supplemental canon source, here is what we know about the pilots:
From "Classified Information":
"A unit called a core is used to eliminate the discrepancies in Eva, a
human being with the body of a god and a soul. The soul of the pilot's
mother, which is placed within the core, acts as a medium and makes
Due to difficulties encountered in the development of Eva-00, the
core's system is poorly constructed, and she falls behind in
performance capacity as a result. Another reason for her inferiority
is that Eva-00's pilot, Rei, does not have a mother."
This makes it plain that with the exception of Rei, the pilot's mother
is always chosen as the Evangelion's soul.
Following this chain of evidence, the almost certain conclusion is
that Evangelion Unit-03 contains the soul of Toji's mother.
The above information is from EVA Geeks.org (Source)
The theory is heavily implied in the series, and there are quotes from the creators to supplement this, but the video games put pen to paper in providing some level of supplemental canon for us.