Rikku's eyes are green with the Al Bhed swirl intertwined in their colour - it's blatanly shown when Auron asks to have Rikku look at him when she asks to become a guardian of Yuna in FFX. The scene occures along the Moonflow, right as you are leaving Moonflow to go to Guadosalom.
As for her eyes seeming to change, it's probably due to the light settings. Darker surroundings or having a light to he back of Rikku will probably give her eyes a much more turquiose look than a green one, so that may be why some people seem to think that she has blue-green eyes.
