Series ending is (SPOILER) alternate universe which Shinji has created in his mind..however it isn't clear in the episodes ending if he accepts the Instrumentality or not...in the movie he doesn't accept it,he accepts the real worls where the one hurts and love another..he decided to stay in the real world..now is question how Asuka survives,maybe she had the will as Yui said...and about the last line on the movie "kimochu warui"...no comment
And the two endings has their own meaning and greatness..Anno knew what he did very well...