So after much more comparison and investigation, I figured out what exactly is giving me such an uncanny reaction to the new model (let this also serve as refutation to the people still claiming this is "just lighting"):

In this side by side comparison, you can see that her cheeks have shrunken back significantly where they meet her nostrils, causing her nose to look much bigger and wider overall. This is nose 4, which I choose because it is the smallest and thinnest option available, so I don't like that it has been given such a larger emphasis in her facial balance.
Here's both traces overlayed on her benchmark appearance for a better visual of what I mean. Additionally, in this image you can see that the shape of her eye has been changed; her lower eyelid has a much more pronounced upward slant. You can see how much of her old eye was cut off by comparing the red and green lines. To me, this makes her look like she is squinting all the time.

Here are the clean screenshots in case anyone wants to judge my linework. I definitely didn't do a perfect job, but the nostril and eye differences are dramatic enough that it doesn't really matter.
Again, I feel the need to ask: Why these arbitrary changes? In my personal opinion the benchmark face doesn't look more natural or realistic aside from textures, and it came at the cost of a pretty large alteration to the overall balance of her face. What would have been wrong with just using the same general sculpt and updating the textures/lighting/etc?
(P.S. if anyone is wondering if these differences are because the faces might be very slightly rotated from one another, I made sure they weren't by selecting the inn background and making sure that not a single background element moved so much as a pixel when I tabbed between the game and the benchmark.)