I know there is a post about Asuka's left eye. But I think there is a bigger picture about the change in the color of the eyes in the case of 3 pilots. It came to me when I also read some threads talking about Shinji's red eyes in 2.22 and the speculation of him being close to be an Angel being and less human, because the only other characters to have red eyes are Rei and Kaworu.
In fact, I think the simplest explanations are often the right ones, certainly even more when you can provide evidence that correlate them : pilots simply take their Eva's color of eyes when in a high sync rate !
CASE 1 : in 2.0, Mari uses secret code "The Beast" piloting EVA-02 (plug cannot be monitored, but Dr Akagi assume that this mode allows the plug to go in a negative depth and enter the contamination level...)
CASE 2 : later in 2.0, Shinji awakens Eva-01 (it eventually leads to merging with the EVA-01 and Rei)
CASE 3 : in 3.0, Asuka uses code '777' piloting EVA-02 vs Mark.09 (we do not have intel about plug depth but the Eva restraints are raised as in CASE 1)
so in both CASE 1 and 3, Mari and Asuka are piloting the EVA-02, and their eyes glow green, which seems to be the color of the EVA-02's eyes :
SPOILER: Show
CASE 1 & 3
And for all the speculations about her left eye, my simple opinion, reading the threads about it and based on the following images is that the eyepatch is indeed a Angel Sealing Hex Glyph device as you can notice the resemblance between the shape (looks like a cross to me) and the color (blue) of Bardiel seen in 2.0 from the plug and the shape and color that appear on the eyepatch and the entry plug in 3.0 !
SPOILER: Show
in 2.0 : Bardiel contamination
in 3.0 Asuka fights Mark.09
in 3.0 Asuka fights Mark.09
CASE 2 : Shinji and EVA-01 : it speaks for itself : EVA-01 have red eyes and so Shinji does when he goes in a negative plug depth...
SPOILER: Show
I rest my case.
PS : sorry if my English is a bit incorrect, I'm not used to English forums already... ( but what a better way to improve my skills in English :) )