The battle with Traumifel is very important, despite how silly the Angel's name is. I... was running low on name ideas, and couldn't find an adequate replacement with a real Angel name. The 'attack' on Unit 01 is just a visual representation of the Angels mental assault. Its show Shinji the nightmare again, probably more intense, focusing on the hatred he fears in others. Eye-symbology is hard to miss in the actual series and movies, so I felt having the Angel's first characteristic be glowing spots of light fit quite well. Effectively this Angel must 'lock on' to a given target to take on his/her fear and apply it against him/her. Naturally, I was most interested in getting to Rei's and revealing Cirus' fear in the battle, so Shinji is dealt with quickly, and Asuka I use as a trade-off to avoid making it look like my new character is taking over completely. Yes, I did intend to do more with Ritsuko in command while Misato tended to Shinji... but it just didn't work out that way *chuckles*. Regarding how the Angel could get to the test-plugs, I thought little justification was needed. Since an Angel was a computer virus evolution machine, the idea of this one possessing LCL seemed as logical as any.
Asuka's fear is a bit of a joke to the audience of the actual anime, especially the End of Evangelion movie. Effectively, the 'nightmare' sequence is the actual sequence from the movie, that I replaced at the start of Kenosis. The author's view of the movie's events is quite clear, yes? *chuckles* And regarding why the Angel doesn't just make itself invincible the whole time... It could only have lasted that way with Asuka for a few more minutes anyway, the timing was such that it didn't have to call her bluff, and it could very well have killed her before that time came, so Cirus' action is still justified objectively in the story.
When Ayanami-sama finally takes aim with her rifle, I had to take care to point out she was not overly afraid or unreasonable. Her fear is losing control to Ikari at the cost of her (now) friend's life. Hence the shot is her fear, not the Angel. Cirus, of course, cuts in for her sake, and takes responsbility. This is why Cirus and Ikari speak as much as they do. I wanted to make the point of her actual fear explicit. Cirus still doesn't presume Rei is overly attached to him, so he maintains an objective look at his life in comparison to defeating the Angel, and enters the fray focused and ready. Of course, things don't occur as he planned, and that cliff-hanger is where part one ends.