There is a changed/removed line in 3.333.
Taken from another post on the forums
^"Antakoso dareyo!" is the scene where Rei asks "Who?" when still incomplete beast mode Eva-02 attacks Mark.09 and Asuka answers "And who are you?! = Antakoso dareyo"
The reasoning behind the removal of that scene seems to be that Wille know that most NERV units are piloted by Ayanami series and so that scene Asuka questioning who pilots the unit is unnecessary.
Even Mari knew that the pilot is Ayanami clone based on the fact that she said "Another you was more pleasant" to Rei Q, so Asuka should know about this too, especially since she's spent more time with Rei than Mari and should recognize her voice.
Edit: There is also another minor change. The code Asuka says is when entering Beast Mode is changed from Code 777 to Secret Code 777 to match more closely to what Mari says in 2.0.