(I stole this picture from one of @Literary Eagle Eva book reviews)
During production Asuka's facial expression in the fight was changed substantially. The original "EoE-like adrenaline rush excitement" expression was scrapped for a more worried/angry/frustrade expression. It's a meaningful change.
Then there's the verb used in the hugely debate "just die/let me kill you/surrender" phrase. While context itself should be clear enough to understand what she really meant, I've also asked the author of the official translation and that's what he had to say about it:
Joseki wrote:0823 Asuka
Just give up and drop dead, Brat Shinji!
can have multiple meaning in Japanese.
are the most common meanings in this context.
While the meanings are different, I felt that the audience would be able to appreciate that Asuka's "let me kill you" has multiple meanings.
In the course of our lives, there are moments when people employ rash statements in moments of passion.
This was one such circumstance.
If we add those two hints/proofs to the already mentioned instances in which Asuka shows signs of conflicted affection for Shinji (calling him for help, calling him with his personal nickname, going to see him for no real reason, Mari's remarks, searching him in the desert, casually touching his face/lip, taking his wrist) Asuka's character is coherent with her initial visual appearance as somewhat hurt and with what Anno tells to the viewer with Sakura Nagashi and the preview. Visuals, soundtrack and narrative really works together to deliver a cohesive product.
Taking away this affection for Shinji not only makes Asuka incoherent as a character, constantly shifting between a rude behavior and senseless messages to Shinji as if she was bipolar, but also makes the movie disjointed with visuals, character and audio delivering to the viewer conflicting messages at the same time.
Regarding Misato and the choker at the end watching the movie I noticed that the "Blood Type: BLUE" notification arrived to Mari came from the DSS choker, so even if Misato did pull the trigger (but I highly doubt it, it wasn't showed) she knew that Shinji wasn't wearing it.
Lurking in this section, I also found an interview from the Q-book with her voice actress that shed some light on her true feelings:
Adam wrote:Q: Especially when looking at Misato's stance towards Shinji, it seems like a lot has happened [during these 14 years].
A: I think there was a lot of pain and spilled tears during these 14 years. It seemed like Misato had overcome this and deleted these memories, but the moment she met Shinji it all came up again. "Please act really really cold", this is what I have been told, but when I did so I have been told "It's so much that it's scary", so I said "Eh, not like this?" (laughs)
I tried to remember the hard time I had in my life, but that was rejected "Normal is okay, don't try too hard to make something up". Despite this, even my normal acting has not been appreciated. So in the end I tried everything, but none was good enough, so I went on with it while asking myself "How should I do this now?"
Q: I suppose there was an explanation by director Anno about the situation or circumstances?
A: As my own age was close to that of the character, I was told to act just like that. For 'Yo' [Rebuild 1.0] I have been told to try harder to sound younger, but this time I could just be myself.
There's this organisation called WILLE, which fights against NERV, and they even have built this magnificient ship WUNDER to [forcefully] get Shinji back and so on... this is from the script, but otherwise it was all my own guess. Only, I totally like the new costume. The first impression I got from the new Misato was "Wow, I really like her. She has turned out to be really cool...", so yes, I really favored the new costume.
I felt like この高いエリ (Kono Takai Eri/This high Ely?), 応援団 (Ouendan/Supportgroup) or Captain Okita from Yamato, so with this costume I'd even do cosplay (laughs). It's really the coolest thing.
Even ignoring "they even have built this magnificient ship WUNDER to [forcefully] get Shinji back and so on... this is from the script" I think it's significant how they tried to make Misato cold but not too cold with Shinji.
Kotono Mitsuishi hit the nail on the head with her description of Misato. She buried the past but when Shinji came back from Eva-01 she was hit by a truck of conflicting feelings and tried to mask it acting coldly (and again, like Asuka, her visual appearance is really on point and coherent with her character). When she had to choose she let Shinji live putting everyone's life at risk (it's an aspect I really hope Anno expand in Final), and she's clearly not some kind of sadist who laugh at Shinji's suffering because it wouldn't make sense for her character and for the movie.