Ooh, subconscious remorse! It's known to happen. Serial killers often show signs of remorse in how they handle the bodies of their victims. (I've watched far too many episodes of Criminal Minds.)

I won't get into the "All Slytherins are evil, and everyone evil is a Slytherin" argument that's all too common, but I think you're right that Barty's a little too subservient and dedicated to be a Slytherin. There's never an indication that he wanted Voldie to win because he wanted the power that it would bring. It was pure loyalty on his part, which does seem more like a Hufflepuff-type personality.

But I've always liked the idea that everyone could have redeeming traits. Claiming that he's just really throwing himself into his role is a little bit too easy of an explanation, I feel, but maybe he always wanted to be a professor. Or if he was one of the kids at school that no one was really friends with, maybe he was using this chance to be popular. Which is sad, and makes me feel a little sorry for him.

As far as the personality-changing Polyjuice Potion effects go, it's possible that particular side-effect starts to happen after a day or so, but they can't become too strong or Barty Jr. would have just become Moody and abandoned his plans altogether. (Character analysis FTW! \o/)