She may be creepy, but I'm surprised people (who generalize) don't find her uncanny. Of course, to us, she isn't (at least, the one's who understand her), but even then, she is rather an alien in human form.
Look at it this way,
From a schoolmates perspective:
-She has blue hair
-She has red eyes
-She's pale as a ghost
-She looks outside the window as if she is waiting for something
-She barely speaks
-(As said by Toji and Kensuke) She hasn't made friends since seventh grade
Doesn't it seem sort of off that it looks like nobody really cares? That nobody just looks at her purely off of this info and says, "What the fuck?"
And then we go deeper, from lets say, Commander Ikari's perspective:
-She's a clone (which I still suspect is illegal) of your now "gone" wife
-On top of that, doesn't even look like her
-You have entire bodies of her in basically an aquarium
-She died twice
-By EoE, her body parts are falling off of her and she's shrugging them off as if they're bruises
-She becomes a gigantic marshmallow person.
Okay, maybe to Ikari, considering how he was part of the Katsuragi exposition and was at ground zero when half the human population was gone AND witnessed his wife get sucked into a gigantic beast (what the hell would that look like?), it isn't so bad, but to us, who hasn't been through that, that would be pretty messed up.
Now, why it would be uncanny: For the schoolmate, she isn't acting like an actual human, despite that she is in the shape of one. Actually, in fact, she barely looks human. There is no existing gene in humanity that can make you have red eyes that almost look like they glow, and blue hair. The fact that she doesn't have any friends is even more uncanny, due to the fact that a real human, despite all the social problems they can have, could at least make one friend. But not her. She doesn't have one. The only other thing that looks like a human and doesn't really have any friends are those moving model dolls that you see in Japan and try to look cute in the clothing they make them wear. And, I might be pushing it here, but.. when she looks out the window... what the hell is she looking at? Is there something there we don't see, or even know for that matter? Could it do something to her? To me? When I put all those facts up front, and then bring the last fact up, it makes sense to wonder this.
Now for Ikari: She isn't your wife. She is the closest thing to it though. The Blue haired, red eyed, albino thing that you have created trying to bring back your wife is the closest thing you have to your wife. It doesn't even look like her, albeit the little bangs she has that hang like your wife. She doesn't even act like her. (as I have reiterated over and over) She barely acts like a human. Yeah, you can talk to her, she smiles a little, but that's it. And that's the closest thing to your wife? Yep. You clutch on to her, but not physically. I doubt you (Ikari) would even embrace that
. Instead, you make a bunch of bodies for the chance that if she dies, you can just make another. That alone, isn't that uncanny?
But that's not all. Not only does she die just to get replaced, she dies twice
. Okay, what human does that
? That's not only creepy, but reaches into the uncanny valley because, knowing that she died, she comes back with a little amnesia and acts like nothing happened. Of course, you know that happens as a sacrifice for bringing her back, but just sit and think about it. That is just wrong, isn't it?
Let's move a little forward, you know, to the point where your about to penetrate her body with your hand straight to her chest.
Yeah, your wife is coming back, but that must feel really weird and inhuman to have your chest in a living body while the person irks only slightly. Actually, it kinda looks like from her face she got molested. But, it's that.
Her pieces are falling off of her. You can see the ends of her bones. You can see the muscle tissue. You can see the pieces of her body that fell off. The most uncanny thing in the valley is a moving corpse. At this point, that is what she is.
That is irking at the least. The funniest thing at that point is that Gendo is acting as if it isn't happening. And then she melds with the stay puft person you keep in the basement becomes a marshmallow person at the end. When I watched Ghostbusters, I was extremely irked by the marshmallow man (maybe it was the special effects, but even then..), so imagine a gigantic, naked, marshmallow lady. What. The. Hell. The thing, which barely looked human in the first place, became with the thing that made humans and became a gigantic white human thing. That actually may make her less uncanny, actually
Although, of course, it is an anime (so it doesn't look like they're uncannily human), so it is okay. To add, we understand, and have empathy for Rei. But, had that been in real life and actually factual and we were all a part of it, I think we'd be "wtf" too. I know I would, and I love Rei.