Because of this, picking out a favorite girl was way harder than I thought it would be. They all have huge red flags and are not nearly as likable as traditional anime girls. But I think they all have some redeeming qualities.
I think Missato is a good woman overall aside from her alcohol addiction. She’s easily the closest character to a normal human in the entire series. Although she's played up as lazy, this falls apart when you think about how many hours she works. She also likely would’ve been a good mother, given that she adopts Shinji and Asuka despite her busy job and not being given any incentive to take care of them. They did have a place to go so it’s not like she had to do it. So if anyone picked her as their favorite I can see why.
Asuka has considerably less positive qualities, or at least that's all we see given the context she's presented in. She’s rude most of the time, but is capable of showing genuine gratitude, like when Shinji saved her for the first time. But that's just one moment in 26 episodes, I can't recall any other moments where she displayed redeeming qualities. It’s also important to point out that Shinji brings out a ton of her negativity due to being totally autistic; she can’t relate to him at all and despises his self-hatred and constant apologies. We probably would've gotten a much better look at her good side if she was paired up with a more typical protagonist. Pairing her up with Rei and Shinji made it impossible to tell if she's actually a good person, so I can't really judge her too harshly for coming off as unlikable. I could easily see her opening up and becoming less abrasive in an alternate timeline.
This just leaves Rei.
It’s easy to see her as a soulless husk, given that the show leads you to believe that the Rei clones aren’t fully human. But I think this is a huge misdirection. She clearly has fledging emotions that could be nurtured into something fully human. I think we never see this happen due to her only interacting with Shinji’s autistic dad and living completely alone. There are a few scenes I recall where she shows more humanity than something that’s soulless should, such as slapping Shinji for disrespecting his dad, crying, getting mad at Asuka for insulting Shinji, and keeping his dad's glasses in her room. Then there’s the scene where Shinji tells her she’ll be a good mom someday after he sees her doing laundry, showing that he saw a lot of humanity in her, given that he's so shut-off and inexpressive, it means a lot coming from him.
So this leaves us in a scenario where Asuka and Rei are basically "I can save her" type-girls while Missato is really the only sensible option.
That being said, I'm still going with Rei.
She's basically an uncorrupted blank-slate. This isn't really something you'd ever encounter in real life, and there's still a chance that I'm wrong about her being able to become fully human over the course of years with enough human interaction, but if I'm right, maybe one day she'd be almost perfect.
That seems like too good an opportunity to pass up.
