Rei is still surprised.
Her stiff expression slowly changes into a smile.
Trajan: This shot makes me smile.
BiQ: And never again could Gainax or Khara top or even reach again this very first rendition of this ultimate heartwarming.
Leighton: My eyes watered at this scene - I actually felt happy at Rei's first expression of joy (in Shinji's presence) as a result of Shinji's care for her.
Rei: "... So he just wants me to smile? If that's what it takes for someone to get a nap around here then fine, I'll comply... but there had better be a good bed and breakfast deal in it."
Kendrix: Congratulations, Shinji! You have been welcomed into the small circle of people who are allowed to see that smile.
The 'blush lines' indicate that this smile is genuine. Needless to say, this is the point where they fall in love. This is, like many other things, emphasized in Rebuild, where they go as far as, for all intents and purposes, holding hands.
thewayneiac: Of course we'll have to see the two remaining installments to know for certain, but I agree they are in love in Rebuild. But if you are saying that they fall in love at this point in the series you are probably overstating it, at least on Shinji's part.
Kendrix: I'm not sure of that - And even if it was to early to call it full-blown love (I do not claim to be above the effects of shipping goggles), at least the romantic-ish feelings/beginning teenager crush must've started in this instant, because... when else?
thewayneiac: I'm not arguing that Rei wasn't in love with Shinji; I'm arguing that Shinji was never in love with Rei. This is, however, the point where they would have fallen in love in a normal show.
Sailor Star Dust: (Re: "...for all intents and purposes, holding hands.") Shinji and Rei first held hands/Shinji pulled Rei out of the Plug in Sadamoto's manga post-Operation Yashima. Evangelion Prelude decided to use that as a manga nod, I guess. (Prelude has a few Sadamoto manga nods: Shinji's rant to Misato about how she and Nerv are selfish is similar to something Manga Shinji told Misato after Kaworu's death.)