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I'd have to same my number 1 goes to Misato, cuz she's just such a noticable charecter, all the little windows we're allowed to see into her psychology, and just the way she changes between the happy go lucky lady to this tough as nails millitary chick. Her relationship with Ritsko (my pick for number 2) is also interesting, I mean one minute they're like the best of freinds, always chatting it up, and the next they're at eachothers necks like nobody's buisness, what's up with that?
A nod to Auska as well, even though she's such an annoying jerk to everyone (I could use another word there, think female canine) and such she really is an important charecter. Without her we wouldn't be able to really see into Shinji, they're interactions give us insight into Shinji's mind, and besides that they're just really funny.
Rei's alright, for an emotionless girl, she pretty much always has this catatonic way of seeing things, and saying things. The world could burn down around her and she's have the same reaction.