THE SECOND IMPACT
Very late in the series we learn what the Second Impact really was.  It wasn't an ANGEL coming down to Earth and causing major destruction, but in fact it acually was an ANGEL coming in contact with ADAM, the very first ANGEL to come to Earth.  That is one of the main reasons that the Evangelions had to destroy the other ANGELs.  This would prevent any other contact with ADAM, which NERV secretly had and Misato didn'y even know about ADAM and the Second Impact.

EVANGELION
Evangelions are part mechanical and part organic.  But what is the organic part? The organic part of Evas are actually clones of ADAM.  Puting in the mechanical part of Eva made it a weapon that can be controled.

UNIT-01 AND SHINJI
Unit-01 was created after Unit-00.  But Shinji was there when Unit-01 was being created.  He remembers his past.  He always blamed his father for leaving him, but actually, after his mother died he chose to leave.  Shinji's mother also helped to created the Evas.  She was also a pilot of Unit-01.  Remember when Shinji was absorbed into Unit-01, well, while Ritsuko was trying to retrieve Shinji, she said that this has happened before but ended failure in trying to retrieve the person.  And also remember when Shinji and Gendou were visiting his mother's grave, Gendou said that his mother wasn't in her grave.  If you put it all together, Shinji's mother was aborbed into Unit-01.  That is why Unit-01 went out of control all of those times.  It was to protect her son, Shinji.

RELIGION
Religion plays a mojor factor in Evangelion.  Throughout the series you may ahve notice that there are many crosses that appear.  Every explosion seems to form a cross, even though that is immpossible.  Misato also wears a cross around her neck.  When all is revealed to Misato from Ritsuko, Ritsuko takes her to the Eva burial ground.  When find many skeletons of what seem to be all of the past failures to make Unit-00.  Each skeleton is crucified.  Also, when we see ADAM for the first time, it is also crucified.

AYANAMI REI
Rei is the First children, which means she was the very first permanent pilot for Eva.  We find that, I think it was, Ritsuko's mother was introduced to Rei by Gendou and then she has this revelation that Rei looks just like Gendou's deceased wife.  So as you may have figured out is that Rei is actually a clone of Shinji's mother.  However, if you think about it, this may be the reason see only seems close to Gendou and then later on to Shinji.  Becouse she is a clone of Shinji's mother, that's why she only likes Gendou and Shinji.