Are there really differences between the story lines of the Rahxephon movie and series? My all time favorite anime is without doubt Rahxephon. I've watched both the series and the movie. As I recall correctly the movie can be considered a summary of the series except for the end. I had a lot of trouble understanding the end of the original series, but on the other hand the movie's ending seemed to be 'dumbed' down.

Is this an incorrect impression of me, due to the summarizing? Or are there indeed differences between both story lines?
The storylines are different.

From Nirai Kanai Online's FAQ:


  the movie is an alternate re-telling of the story. ... In other words, the movie and TV series are not in the same timeline, each one tells its own different version of the story. ... It is not a good idea to use the movie to find answeres (sic) raised in the TV series. They're two different universes.


As a concrete example:


   In 1998 the twins Ayato and Itsuki were born, they were brought together by Quon's and Shirow's DNA --in essence, Ayato is Maya's nephew. 


(in the anime; from NKO's page on Maya)


   in the movie Ayato was her (Maya's) real son


(from the FAQ again)

A note about the source: The site is by far the most exhaustive reference for RahXephon I've found, but it doesn't cite any sources. It could, theoretically, be nothing more than an elaborate fan wank.