One thing I'd like to point out that unlike replacing Gendo, for whom any Magnificent Bastard would do; Ritsuko Akagi is deeply involved in building the Evangelions, its weapons, figuring out the Angel's AT-field dickery, and checking up on Rei. This means whoever replaces her better be a damn good geneticist and biomechanical wizard, for if the job is foisted off to someone else... then there's really little point in replacing Dr. Akagi. Might as well just make up a new post for NERV.
Strangely, for this situation I feel an expy of Orochimaru would actually work best. Angels and Evangelions are functionally immortal, after all.