Hmm what if it is just one "thing"? Like in that Game "Miasmata" [url]http://www.youtube.com/watch?v=2FGr_Zyc5-g[/url]. A invincible threat that forces both of them to get thier shit together, to work together and to face their fears?
And you guys are right, turning Shinji into a survivor whould be the "make it or break it" point of the story.
Well, if you go here, there is a way to make the story even more interesting :
the ending of Miasmata very strongly imply that the Creature is actually an hallucination produced by the plague-ridden brain of the player character, and that he is the one who killed all the scientists in the island in a fit of insanity, before forgetting everything he had done.
You could turn the story on it's head in the same way : Shinji always encounter a "creature" trying to kill him, and desperately tries to protect Asuka against it, who for some reason always seems to fail to detect it, which make her think that he's gone mad and is imagining everything... until to her horror she realize that he did gone mad because of some illness related to his experience in Instrumentality, and the "creature" is the manifestation of Shinji's illness's and slipping sanity, which is trying to make him murder everyone around him, meaning Asuka!
Cue the last chapter shifting the POV from Asuka, desperately trying to escape a completely crazed Shinji and find a cure for before he finally finds her and kills her... or she will have to kill him first! From time to time switches the POV back from a Shinji completely tripping balls, thinking that Asuka is the creature and that he must kill it before it harms her, or maybe he'll see Asuka as Gendo and will want to take his revenge for everything he has done to him and the rest of the world, or maybe make him revert back to an rage-filled animalistic state where he thinks he's a berserk EVA-01 reviving his fight against the Angels, Asuka taking the form of Sachiel or Zeruel.
after seeing Asukaner117's last post just above, I've another idea : make it happen not in a post-3I setting, but in a post-3.33 one! Asuka, Shinji and Rei Q are resting in a ruined building in what was once a little city in the suburb of Tokyo-3, before being attacked by some horrible creature born from the failed Third Impact, a sort of "little" FoI that somehow survived the failure of the Impact and is now tracking the trio.
Asuka is alone, without combat equipment except an utility knife in both Shinji and Rei Q's backpack, with Shinji still in catatonia and Rei Q not really good on initiative, stranded in a city completely turned to core in which nothing is usable anymore and which is the hunting ground of the "thing".
First she'll need to make Shinji snap back from his BSOD, and then find a way to escape from the thing before it finds them or they have to use more of their meager rations, which will diminute their chance of making it alive to a location where the Lilin could pick them up!