There's still the modifier cascade. Dexterity damage, in 3e, didn't just affect your skills but also modified your Reflex saves, AC, Touch AC, Initiative, and possibly other numbers as well (such as your attack bonus if you had weapon finesse). If something was hitting you with ability damage every round, that meant a fair bit of recalculation, much more than you'd have with a (non-stacking) flat penalty. Feasible (though nonetheless annoying) for an experienced player, although even they would occasionally forget to note some aspect of the penalty, but utterly nightmarish if you're dealing with new players. I speak from experience. It's one of the biggest reasons I dislike ability damage.