but not like any ordinary women or mother
Bold of you to assume that "good parent" is somehow the default setting. Shitty mothers abound as much as shitty fathers, its just that social constructs on average make it easier to get away with slightly different "crimes".
One clever thing EVA does is that it has the characters superficially seem like one archetype & then reveals parts that don't rly fit with that, to go with the whole "ppl are complex and not completely predictable" theme.
Yui's no exception - Shinji vaguely remembers her as this generic archetypical mother figure, (well of course - he was only 3 when she died) and lowkey blames Gendo for getting her killed, but then we learn that she was actually one of the scientific masterminds.
It's no coincidence episode 16 is named about some concept in psychology when small babies (& certain mental patients who didn't have proper care AS babies) will tend to see ppl - and initially their parents - as all good (when they get food, affection etc.) or all bad (when they're being scolded)
That said we should get some nuance in there.
While you shouldn't have kids unless you have the time & energy & temperament necessary, ppl with children are allowed to still have a life outside them & a career XDD
When Fuyu first meets her she was hoping to become a housewife & have multiple kids. Something happened to make that impossible: Adam was found within her lifetime. If she didn't prevent the apocalypse, there would BE no future world for Shinji to live in. She does say that making sure he gets a future is her big motivation.
So she was in a situation where what she thought the best way to protect him (and Gendo) meant parting from them.
It's like that one bleach poem:
If i don't wield the sword I can't protect you
If I keep wielding the sword I can't embrace you
Judging from her line about "people are easy to destroy" she thought she was gonna be disappeared when she volunteered to be the test subject, so waiting until later probably wasn't an option.
Of course wether it really was the other option or an acceptable sacrifice is a whole 'nother question.
I mean, Gendo believes instrumentality is "the only way." and has it rationalized that it's the best for everyone and that Shinji, Yui and Rei will understand when they're all reunited as one happy family of LCL puddles.
Sometimes one has to make hard decisions but there's enough times when ppl get stuck in a scarcity mindset or culturally accepted norms even though real proven alternatives exist.
One way to view her is a not fully reprogrammed former cult member. She was brought up by SEELE members, decided their ideology was BS, but she still sees the future predictions as inevitable - they have to 'technically' fulfill it. Hence, doing third impact but undoing it immediately after.
It's unclear if she's even wrong, maybe predestination really does exist in that 'verse.
Maybe she thinks of being "the chosen une" as an honor. Even Gendo seemed more concerned in that flashback, he was like "omg the poor kid will have to live in this crappy world" and at least in the anime 'verse made sure to give him something like a normal life by duping him off with a professional child minder.
That said, I'd agree that the main difference between her and Gendo is that she has social skills. They're actually very similar, that's why they got together despite their different ages & social backgrounds. I guess I see Gendo himself as more grey than full on evil so Yui would be no different.
She's definitely way greyer and more complicated than the simple benevolent perfect mother figure Shinji first remembers her as.
I'd always wished he had more of chance to comfront her. Even if he forgave her in the end, I'd like to see him be mad at her for a bit & get a more differentiated view of her.
The closest we get is that bit in ep 25 and i guess when he names her as one of the many ppl he can no longer trust in Q.
I'd agree that Misato probably knows him a whole lot better than Yui ever did/ did more actual parenting. It seems pretty unlikely that she would ever have had bio children of her own under other circumstances judging by her general personality & lifestyle but despite all her flaws, she cared enough to at least try.