Putting Unit 01 in space keeps it safe from Wille's anti-Eva crusade and keeps Shinji out of Seele's hands. As long as he's in the core, they can't risk getting him back without putting Unit 01 back within Gendo's sphere of influence. Unit 01's kind of a liability for their plans now.
Bagheera wrote: Do we know that, though? The scenario this time around seems to be very different. I'm not sure Gendo's motives are the same now as they were before.
The scenario for Shinji and Rei was written before Yui "died" and her disappearance into Unit 01 seems to have been planned all along with this Gendo aware that it would happen. I really get the impression that he and Yui are working toward the same goal, whatever that is. He says they'll see each other again soon, so a reunion of some kind is evidently part of the end game.
What I don't get is where Unit 13 factors into his plan. He was adamant that they awaken Unit 01 as quickly as possible after Seele spilled the beans on Mark.06 and their goal was in sight when it did, but then in 3.0 he completely shifts focus to Unit 13 with no mention of Unit 01. What purpose does it serve when Unit 01 has Yui and Rei? Is it just a power source for the flying pyramid? If Unit 13 is actually the Key of Nebuchadnezzar, maybe it was part of the plan all along and circumstances pushed it back.
Someday I hope that we'll be reunited if that is what's destined to be. Perhaps we'll discover that elusive bible. And then we will finally be free!