1:54 split up dialogue for "Is he.." and "going to skip school again" also subs fade too fast
2:10 "Shinji-kun?" instead of "Shinji-kun?!"
8:23 comma after "cruel" isn't needed
8:28 "fourteen-year olds"
8:34 "So, has he called" should fade earlier
8:44 "What are you going to do?" should dissapear when the scene changes
8:47 "Not really." should fade earlier
9:51 "I see." isn't really needed since it's barely audible 
10:01 more succinct tl? Also, the sub should fade when the scene changes
10:04 "But we need pilots" should fade before scene change
11;01 "Touji..." little bit late
11:06 "His little sister scolded him", also needs to fade earlier
11:29 "there've been more..." should fade earlier
12:12 "Huh? I guess."
12:58 sub should fade earlier
12:59 "Yes." should fade with scene change
13:09 period instead of !
13:11 "But like I said, they were..."
13:16 "so what?! Don't you..." should fade with scene change.
13:17 "Sissy, pervert, ape!" should be one line?
12:35 sub should fade earlier
14:02 "If I say that I won't pilot it, what will you do with it?" I personally don't hear "Unit 01" explicity
14:23 "... To begin with, it's not something that comes naturally to me"
14:27 "But Ayanami, Misato-san and Ritsuko..."
15:00 I don't hear "Unit 01" explicitly
15:47 "Ikari! You forgot this!" should be one line
16:06 "Thank you" should fade with scene change
16:51" "Ouch!" should fade with scene change
17:39 "Take care" should fade earlier
17:40 "Well..." should fade earlier
20:18 "Look!" should fade with scene change
23:15 "Shinji is at a loss trying to understand this girl..."