It's true that the ideal beauty changes with the time and the culture, perhaps she was really considered beautiful at her time, but other ladies who were considered beautiful at a similar era are still considered to be beautiful... although beauty is quite subjective.
Well, about her melancholic eyes I've read that weren't considered by many beautiful.
Although this of not being photogenic could be another good explanation, in all her portraits she looks wonderful but on her photos not very much...
It's true that Eugénie herself was hating her melancholic eyes, and was always putting make-up on her eyes for correcting these "dropping" lids, because she was saying that gave her a stupid expression!
In fact what all contemporaries say often about Eugénie, is that all her movements, all her gesture, all her bearing, were a miracle of grace, majesty, and elegance... I would like to write here the rapturous descriptions made by Queen Victoria and by the Princess of Metternich about Eugénie, but I don't have the books here, I'll take them later.
I think that this kind of beauty can't be captured by a photo. A photo is just showing the face, and if the face is not perfectly regular, people just see that, and don't understand what is so amazing in this woman. That's why Eugénie's photos are a bit disappointing.
Only good painters can convey this kind of beauty. That's what Mme Vigée-Lebrun made with Marie-Antoinette (if you look at Wertmüller's portraits, he just was able to copy unimaginatively the features, not the grace at all, and Marie-Antoinette is rather ugly on these portraits).
What Vigée-Lebrun made with Marie-Antoinette, Winterhalter (above all) made it for Eugénie... If we want to understand what Eugénie was, we have to look Winterhalter more than her photos.
But as far I'm concerned, I must confess that I find her beautiful even on the photos... More interesting than Sissi, who was perfectly lovely, but (IMO) icy, frosty... I know that a lot of people won't be ok with me about it... but as you say, all is so much subjective about beauty...