>>6421511EoE is the real ending of the series, not that zero-budget clusterfuck art project that were episodes 25 and 26. Anno and Tsurumaki have said that it was a cop-out they HAD to make, when they were under intense pressure of time, money and the Standards and Practices Department of TV Tokyo blowing behind their necks.
No contest regarding Matrix 2 and 3, actually. They suck, although that has a (lame) explanation as well. It involves BDSM, sex change, divorce and a man with a vagina:
http://lecter.org/forum/showthread.php?t=248