The way I see it is that Jean has had her time to shine from 1963-2003 or whenever it was. Rachel was created to be like Jean but, you know, more interesting, so, they should just use her as the perennial Phoenix, telekinetic, Grey family member of the X-Men. She has well forged enough relationships with most X-Men and has more interesting personality anyways.
Also, I often hear people say that Rachels background is confusing, and it isn't really, she is just from an alternate future.....no more confusing of a background than 50 other of the X-Men roaming around...I would argue that Jean Greys background is more confusing, what with the "telekinetic cocoons" floating around Jamaica Bay and "Phoenix simulacrums" that took her place and all.
So yeah, just leave Jean dead in favor of Rachel.....no more of this Phoenix 5, White Phoenix, Hope Summers, Teen Jean BS. Just Rachel as the Phoenix please.
It's interesting that Legion is just simply known as Legion these days despite the fact that was never really his codename or whatever. As you mention in your review, it's just the name of the story he is in as it is a quote taken from a story in the christian bible.