Doctor Doom û Honestly I see Doom, kicking Gendo out of the command chair and taking the whole operation over. His plan is to protect earth from these creatures and if possible capture their power for himself.
Darkseid û Well since a large chunk of the anti-life equation is on earth, itÆs not in his best interest to let the world be destroyed, so I see him sending Shinji back, accompanied by parademons and maybe Stephan Wolf, Granny Goodness or Kalibak for back up.
I see this Shinji kicking out Gendo from the command seat as he solves the Angel problem (killing or capturing them) while searching for the anti-life equation.
Galactus û I just have this image of Galactus grabbing an angel between thumb and fore finger and saying ôAh, hors DÆoeuvres!ö
A Shinigami from Death Note û I just like the idea of Shinji beating each of Angels by writing their names in the note book.
The Emperor of man (WH40K) û He should be kicking around somewhere during this time period and if the Angels are daemons then heÆd take an interest in their destructions
Slaanesh (WH40K) û If the Angels are Daemons of Khorn, I can see Slaanesh sending one of his favored sons to stop them.
Batou (GITS) û I figure section 9 would have most of Seele in custody or dead about half-way through the series.
Beatrix Kiddo (Kill Bill) û HeÆd be a much better fighter when he first arrived.