But he didnt know her well his fixation was due to guilt and trauma and the Hexcore used it. And to cement that when she fades when Victor says I'll miss our talks and she says no you wont her voice gets robotic. Like how Victor is in the full robot form.

And she appears after Victor leaves says he won't pursue Hextech because of Sky. Who then shows up to encourage him as he uses more Hex Tech? Sky
Perhaps Victor may have noticed the differences more if he'd known her better gotten Uncanny valley

The Hexcore is using the image of Sky from Victors memory but still it can't help but remove her glasses. It's not like she's a ghost and therefore naked or something. Eventually she glowy with no clothes but for a while she was like this. Clothes but no glasses.

But while it starts off focusing on imperfections that might improve the quality of life of people when they are altered, Sky already had a accommodation she had glasses for her bad eyesight and still they are removed

There is one big thing that's different from Sky in season 2 compared to when she was alive and even Sky in Victors memory and that is her glasses. The Hexcore is obsessed with perfection it starred off with fixing Victors leg after all.

She looks less similar to her former self

Very similar to how she looks in Victors's memory. Though even more confident looking than even his memory of Sky.

After Victor leaves Jayce he begins hearing Sky then as he uses more Hex tech seeing her and she looks like this

Compared to when she was alive her bun poofier. Her eyebrows are are less thick at the ends. And she's making direct eye contact Victor wasn't close to her wasn't always watching her. So doesn't realize she's shy and flustered.

He even goes a separate way from Jayce when he continues his research after he wakes up from his coma he remembers Sky when he makes that decision but he remembers her like this

Her notebook makes Victor appreciate her ideas and mourn her loss of potential but he never got to know her she never got to know him. She watched from afar and all he has is a notebook. But he feels guilty tries to do right by her by telling Jayce to stop Hextech

When she finally goes to have a proper conversation with him about her research she's rehearsing her conversation. Unfortunately she is never able to have the conversation. Victor is left with only her notebook.

She had a crush on Victor but she was shy. She was always looking from afar. She and Victor weren't really on close terms they didn't really talk much as a result. But she's inspired by him. She often averted eyes or ran away when they made eye contact