A lot of suggestions for changes of the characters in this thread.
Personally I wouldn't change much about the characters. I'm actually happy with them as they are. As I see it, they are the best characters in any Star Trek series.
The few changes I would make are:
I would give Chakotay a real tribe and re-write "Tattoo" as I mentioned in an earlier post. No "sky spirits ancestors".
I would give Kes a human lifespan instead of that nine-year thing that didn't lead to anything. Since I fixed that in my story "Coming Home" which would replace "Fury", it would be no problem.
B'Elanna wouldn't be tamed so quickly. Therefore I would put in at least one episode between "Caretaker" and "Parallax" where she still should be something of a Maquis hothead, negative to be aon a Starfleet ship.
Harry would be more like he is in the books where he's actually doing something. However, I would avoid having him injured as much as he is in the books.
As for the other characters, I would keep them as they are.