Ultimately, what's really scary about her isn't that she doesn't care about you - it's that she cares very deeply about you, or more specifically, how you can gratify her ego. From the very point where her morality blockers are removed, it's made clear that she's evil because she wants to be evil, and all of her traits - hubris, egomania, effective insanity - are all traits you find in human villains. What's even worse is that her general creepiness comes from being the exact opposite of a typical rogue AI It's not because she's coolly logical and mechanical, it's because of how passionate and human she is.

Combined with her actual dialog (which includes a number of concerning threats and boasts of how she'll destroy humanity), listening to her speak will continually haunt you throughout the game.

She'll also occasionally whisper to you, which comes off as incredibly discomforting. This will often result in her speech slowing down and/or becoming deeper to draw out the threat. One example is if she's intimidating you. Every impediment is timed just right in conjunction with her lines for maximum effect. Her Electronic Speech Impediment constantly gives off the impression of her instability along with just being creepy in general.

The way she speaks is enough to make your skin crawl.

If you value that meat, you will do as I tell you!' 'It is my will that gave you your cybernetic implants: the only beauty in that meat you call a body.

Worm/human hybrids system shock