I know what you're talking about and I have the answer: It's because the eyeball texture was changed to look more realistic and veiny. There's a pinkness around it to replicate flesh, that might be what you've seen. The old texture was just greyish and flat, no veins or pink at all.
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RE: Eyebrow Changes
Not playing Miqo'te, but I thought I also had grey eyebrows instead of white. However, looking closer it looks like the eyebrows are instead
thicker now.
This is just in my case, and not related or the cause of the issue on Miqo'te and the least of my concerns as my hairstyle covers my entire face almost, but i'll point it out regardless.
Top: Old / Bottom: New
God, I miss those old scales.
Really, it's like they've used the paint bucket tool underneath the texture as opposed to colouring the hairs and that's giving the impression of "darker eyebrows". I also reported this change during the Benchmarks.
I'm sure they chose to do this because they wanted to go "realistic/high definition" but it doesn't really fit Au Ra...
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Each time I open the Endwalker benchmark to get some screenshots, I feel so sad. I'm always thinking "Oh so that's where you've been." when I load my creation data.
It would be nice to hear something from the development team about all of the things discussed thus far.