@syz: The film seems to be a continuation of the series post episode 24. I always took it as either the events of episodes 25-26 and EoE were happening concurrently, albeit one having a happier ending and happening in shinji's head. OR 25-26 was just how it was meant to be and none of the robot stuff mattered. Granted, Anno put the death threats he received in EoE as images, so that whole thing could just be a giant fuck you to the fans.
Though I could just be on dust.