Charlottesville is my old stomping ground, and although I occasionally visit, it's been so long since I was in C'ville on a regular basis, I'm not familiar enough to be able to recommend where to live.
I do suggest avoiding areas around the downtown mall. The mall itself is rife with vagrants and is sketchy after dark. Unless you're with a group of people, the downtown mall is best visited during daylight hours. I'd also suggest avoiding the areas around Jefferson Street which is mainly low-income housing, and in my day, was the part of the city we avoided venturing into.
Traffic along Rt. 29 is congested during rush hours because of the many stoplights, although they are timed pretty well. After living in NoVA, I find the congestion in C'ville a non-event.
Students are going to live as close as possible to campus, so I don't imagine a large population of students living at someplace like the Greens at Hollymead which is outside of city limits.
I suggest taking a Saturday and visiting the apartment complexes you've listed to get a feel for the neighborhoods and amenities.