Asuka. Rei popped up in Shinji's vision for a second too but that seemed more like a vision than what was actually happening.
The whole eye color thing is just a production issue that people read too far into. It's Asuka, and the bandages are where she got hurt during the production model fight.
The thing with that particular ending is that everybody melted into one mind again but Rei says that basically anybody who wants to be alone enough can separate. Although I'm sure she puts it a little more eloquently, talking about finding hearts and stuff.