I don’t think this is what Nomura had in mind when he designed their eyes. But I don’t think it’s a coincidence the women of Final Fantasy X have remarkable eyes. Look at this:
Lulu, being generally fair-skinned, seems to have albinism due to insufficient production of melanin. But it’s not that her eyes themselves are red; her iris is transparent enough that the blood vessels behind it show through, creating the reddish color. The lack of melanin means her retina is less efficient at absorbing light. Lulu probably has photophobia, an uncomfortable or painful response to bright light. This can lead to eye damage. Note: Paine has the same type of eye design.
Rikku seems to have two conditions: Spiral in the Eye and Polycoria. We know the condition is known as Star in the Eye, when cataracts to form after a blow to the eye. It’s coincidental, so who’s to say it wouldn’t have become any other shape. Polycoria is when one has two or more pupils in one eye. I speculate the pupils form a spiral shape to follow her “Spiral in the Eye” condition.
Yuna has heterochromia, which is a difference in color between the eyes (that’s apparent). But she features a circular ring of color around the outside of her pupil, known as central heterochromia. In this sense, like Rikku, she has Spiral in the Eyes.
And while I’ve never seen her cry, I wouldn’t be so surprised if Paine had Haemolacria (in addition to albinism), a condition in which a person cries blood. I don’t know, she just seems so edgy…
Like I said, I don’t think Nomura was trying to pattern their eyes off of actual medical conditions. I wonder why Nomura chose to give the ladies these cool looking eyes?