I think complich8 is dead on as to saying it was Shinji's angst....
If you think about it...End of Evangelion is similiar to Tombstone.....Everyone dies!!

But i think it is one of the best movies i have ever seen anime or real, but warning to people who do watch it (lol too late now) your going to be confused, sad, depressed and a whole other wack of emotions...i had to watch it twice to understand it fully, great movie indeed!