Among other things, the score/battle ability of KoF99 is based on amount of energy left after the match, # of hits delivered, straight win or not (in team battles), perfects, points for normal moves and specials and of course the difficulty setting. (S)DMs also count, but only if they connect, otherwise you will get points down (accuracy). (S)DMs also don't score if you manage to break a cancel and kill an opponent with it.
Strikers will ruin your BA score. A preliminary striker attack/combo BEFORE a DM for example would reduce the points for the DM to 0.
Play it on EXPERT, win with at least half of your energy left, and/or do a straight win with one char against all opponents of one team, and then watch your score/BA go UP. Chain combos also greatly increase the score.
Ah yes, and keep in mind that different characters score differently, so try to substitute your char, you'd be surprised.
Btw., I think there must be some kind of Battle Ability FAQ on dhp. At least I saw it in the threads there some time ago. Not sure about this, tho.