They cut Pen-Pen because the scene where he was introduced involved Shinji being naked in front of Misato, and because there were lots of beer cans in many of the shots he was in. That was only one of many dastardly cuts made for the show's Toonami run, which I will not suffer people the memory of.
Anyway, Pen-Pen should be an animatronic puppet. That way they'll have full control over his actions, and the actors will not have a hard time interacting with him. Plus, it ensures that he can look identical to his Anime counterpart, since Pen-Pen is supposed to be a new breed of penguin (therefor not having an adiquet living counterpart). In some shots he can be CG, but for the most part I think they should use the puppet.
And on the topic of the original post... I think that they should portray Rei as an asian albino. That would explain her pale skin, red eyes, and light hair. The question though, is will her hair be pearl white, or will they tint it blue? I did a re-color of a Rei cosplayer pic a while ago where I tinted her eyes red, lightened her skin, and bleached her hair to a light shade. Here are the two versions, one with the more "realistic" pearl white hair, and the other with the less believable but more anime-accurate blue tinted hair.
Rei's alleged albinism would obviously just be a cover story for the fact that she's an angel, but I think it would be a very wise approach for the character. I think it could give the audience a little more understanding as to why she's so withdrawn, and give some partial reasoning to why she is a a social outcast.