they put the big 4 into bodies, but X was nowhere to be found.
And by the time he contacted the resistance in Zero 1-3, Im pretty sure he doesnt have the materials to make a fit body for him. Not to mention the TIME to do so when theya re constantly under attack and attacking key NA areas.
X's death in Z2 only proved that X just no longer wanted to return to the fight. He was dead tired (no pun intended) of his centuries long battle. He had no intention of regaining physical form. His body's death was also of no real bother to him.
He had gained much higher powers as a cyber elf as well, with the ability to project a barrier over the entire resistance base to protect them from Dark Elf's influence.
Well, not exactly.... At least from what I understood from the storyline, They all had a game plan; X was to protect the Mother Elf (or Dark elf. Which ever you perfer), and Zero was to try and stop Elpiso from reaching X's Body... of course you know how the story went during this time. It just goes to show that Zero really couldn't save the important people after all... (Sorry... Mega Man X4 reference) At least, that's what I gathered.
The reason why the plan failed was because Zero was slown down and Elpiso had both the baby elves with him. Seriously, How could Zero prevented this?
Secondly, Ceil did create Copy X's inital body. With that said, she must still have some blueprints on his design either based of Weil's design or that of the late Thomas Light. I just don't see how they wouldn't be able to recreate X's body.