I will admit this, the manga really does adapt these parts much better than in EoE, which is no small feat. Shinji's realization that the world in which he lived in was imperfect, but its the moments of despair and overcoming them that makes those moments of happiness that much better. Really masterful of Sadamoto to use those memories in the form of photos. Wonderful.
Unfortunately that means Rei will disappear from this new world. The way she fell over in the new world was pretty synonymous to snowfall, something Yui talked to Shinji about. Brilliant storytelling.