In the english version I think he doesn't really become your lover, he just says he likes you and wants to be with when he is older. That is what I read anyway I could be wrong.
Oh and about the final scene:
! In a new game plus you can choose who you want to spend your last moments with if you have a max social link with then, but only the boys of your party(but not Jumpei because he can't be your lover).
! Many people go with Shinji(if you can make him live) for obvious reasons.