(If u don't agree with me, feel free, sorry I know I overstate my case a lot of the time!!)
Frodo in the book is a lot less waifey and pathetic. The last time I was reading it I definitely saw him as ISFP. There's a line in there about "people would mistake Frodo's kindness for weakness" but when he was crossed, look out, etc. Gollum tries to fuck with him and Frodo gets pretty pissed and has a few choice words with him about how the ring will be used to force him to chuck himself into the volcano if he doesn't behave. Also what about the stunt in the inn. "Woohoo, I'll have a few drinks and get up on the table and put on this uber secret invisibility ring in front of EVERYONE!!" If you ask me that was a goofy SPish thing to do! Nearly got them all killed. And in the book it was FRODO who used to nick mushrooms from the farmer as a kid (not Merry and Pippin). He's not some angelic otherwordly martyr like in the film.
I think ISFPs have a stubbornness and a grim determination to carry out their mission once they've seen that it's right and only they can do it. Harry Potter shows it so many times. Frodo certainly has it. He takes fucken ACTION. I dunno if I see INFPs behaving that way. Frodo DOES understand the danger, all the way. He just knows deep in his heart that he has to do it anyway. Harry does this all the time too. They are both action heroes who hang on stubbornly beyond the point of all rationality because they know they have to. In my mind that is what an ISFP hero is capable of. Inside their heart is breaking but they just keep going because they know what is right and they are just too damn stubborn to give up even if it doesn't make any logical sense.
As for Shinji. Shini is a gentle kid who is depressed because his love and trust has been violated by his (INTJ?) dad, who doesn't care about him except as a tool. He is very shut down and really wants to be left alone (typical ISFP under stress). He has no insight into anything, no goal or plan or vision, I don't see any Ni there. He never gets lecturey with anyone (which would be FJ) but has got a smart mouth with authorities (SP).
Misato: "How could you endanger your life like that?!"
Shinji: "It worked, didn't it? You wanted me to pilot this thing so get off my case already."
I'm reminded of the episode where his friends get in the Eva with him - he flips out and attacks the Angel with his knife when he's nearly out of power, even though he's been ordered to retreat. This is the same kind of "irrational hero" behaviour that I was talking about above with Harry and Frodo.
Anyway I could be wrong but that's how I perceive ISFP protagonists. I think they rock.