You want to force a relationship were none exist. Of course, it doesn't mean that none can exist. But it isn't automatic. If there is to have a relationship between them, it need to be built. It can't just be based on a non-existent blood ties between them like if it was a given.
And no, 616 Jean isn't identical to 811 Jean. For one thing, she choosed to kill herself instead of risking losing control of the Phoenix while the other lived. Seems like a big difference to me.
And yeah, the writers mostly ignored the nonexistent relationship or had the characters make joke about it. It's some fans that absolutely want those characters to have a mother/daughter relationship where none exist. Havok83's point is correct: they nearly never spent anytime together and couldn't have learned to know each others that much. (which is exactly why recent writers made jokes about it)