Or... the Unit-08 armor. My current theory is that they will implement some of the sweet, sweet technology used to get the Mark.06 under control to make Eva-01 manageable once again, and that's Eva-08.
Given Nerv's current state, Gendo can't really do much besides furrowing his eyebrows at any possible enforcers Seele might send (some U.N. troops, for example). Unless they pull a page out of the manga, and we get Super!Gendo somehow.
I find that hard to believe, having Unit 01 being remodelled would be like turning Optimus Prime from a Firetruck to a Ferrari, sure it's a bit of an upgrade, but COME ON. It just breaks tradition, Eva Unit 01's been a big symbol of evangelion, the cross of science and technology and religious belief. Without Unit 01, Eva just isn't Eva.
The only way I think that Anno would be able to pull off such a stunt would be to make it in a way that Gurren Lagann did, when Kamina died. You'll remember him none the less but Simo takes up the flame and continues to be even MORE epic. So if Yui has to done the armor of the arbiter...I mean umm, Unit 08, then she better raise hell.
On the path to Universal Understanding.