The major line in this episode is Asuka asking why Shinji wasn’t sent out for her.
Being saved by Shinji is something Asuka can accept. It’s happened before. Being saved by Rei, someone Asuka views as only a puppet, is unforgivable. It’s something which leave Asuka unable to forgive herself. At least Shinji she can take it out on if he’s the one to save her, but Rei she can do nothing to.
If this Rei is a third Rei, then the Rei seen since at least the second episode would be the second Rei. What about Rei seen for a moment in the first episode, only to vanish? Why did she appear before Shinji? How did she appear before Shinji? Is there some manner of link from one Rei to the next? If the clones were used as parts to put Rei back together, does this mean the Rei Shinji knew was the one with Rei’s soul, a second Rei patched up from the first Rei after an incident?
Kaji is gone. Rei is gone. The origin of Rei, Adam, the Evangelion, is all made clear. The remaining resolve are Seele’s plans for conclusion, the finalization of Gendo’s efforts, resolve for Asuka, and resolve for Shinji and his father.