Rahxephon wasn't EVA done right,as they didn't share any similarities,beyond the robot theme.
Shinji was a tool used to unite humans as one entity.
Ayato on the other hand returned Earth to its former self, before the Mu invasion.
Also, the romance in EVA was rather shallow,and the fanservice very predictable (nude Ayanami falling over Shinji anyone?), while the romance in Rah on the other hand was very real.