I honestly wouldn't mind her not having any points what so ever in her classes. Just because it makes sense that she'd lose a lot of her skills over the time as far as the classes go. Most of the Classes, if you noticed, are book knowledge more than spell casting knowledge. I'd think if Bella had skills in Runes or Arithmacy, she might have lost a fair amount of that knowledge over time. I also think of spell casting to be more intuitive but that's just me. She also may be gaining more of her knowledge back over time as well. I personally would put her majors as Runes (simply because I think that's something lacking explicitly in Voldie's army) and.... either Care of Magical Creatures or Arithmacy. She would have Others as Muggle studies (obviously), History of Magic, Divination, and Astronomy, perhaps? Minors could be Potions, Herbology and either Care or Arithmacy. I also am of the opinion that Bellatrix was fairly intelligent, even if a bit obsessive, before she went to Azkaban, so take my suggestions as you will. :)
Charms and Curses seem particularly important to her. If I had to guess which academic subjects mattered to her, I'd guess along the lines of CoMC for some reason, possibly History of Magic as well.
All I have to say to the History of Magic is Binns. It takes a special kind of personality to enjoy History of Magic after going through his class, even if it does kind of make sense considering the Black family.