Shooter wanted Jean dead because Byrne drew people on a planet that should be not have people. That is the reason Shooter wanted her dead, it wasnt like he thought the dead was something special.
I think the original writer of X-factor wanted Jean back and the next writer, Weezy, was also alright with that decision. Claremont wanted Jean's sister, Rachel simply doesn't fit the thematics of the book
I think the intention of getting rid of Phoenix permanently, but on comics nothing is permanent.
So it is funny to me people saying X should stay dead, because to this only Gwen abd uncle Ben stayed dead
The whole problem of Phoenix is that it go overused too much in bad stories in only 15 years.