Damage Types
Shadow Naoto does not have any damage-type weaknesses. She is resistant to fire damage and completely nullifies light and darkness damage. Physical, ice, lightning, wind and almighty damage all function normally. The lack of an elemental weakness does give you a bit more latitude than most bosses, especially since Shadow Naoto does not favor a particular damage type.
Dekaja
Shadow Naoto becomes significantly more threatening for three turns after using Heat Riser. This skill significant increases her attack, defense and agility attributes, making her a much more potent threat. The bonuses from Heat Riser can be completely removed by casting Dekaja on her. You should almost always be able to cast this before she gets to act. Not only does she lose the benefits of Heat Riser, but she now has wasted the entire turn she used to cast it.
Elemental Weakness Exploitation
Shadow Naoto's exploitation of your characters' elemental weaknesses can be one of her weaknesses. Her elemental spells are her only real method of killing your characters. Her nonelemental attacks are not as effective as actually killing her target. She does not cast elemental spells as often on characters without elemental weaknesses. Even if she does, these spells are far less potent without the extra damage from the elemental weakness. Using characters and personas without elemental weaknesses, such as Black Frost, significantly hinders the AI of Shadow Naoto.
Healing
Outside her elemental spells, Shadow Naoto, does not follow up with killing your characters very well. Brave Blade and Mute Ray only hit one target and should not kill a character at full health. Galgalim Eyes is completely unable to directly kill the target, but does set his health to one and casts the Enveneration debuff. If you deprive Shadow Naoto of Heat Riser and attacking elemental weaknesses, those are her only options of attack. Heal any status debuffs and damage caused by these abilities immediately. This results in Shadow Naoto repeatedly using the same attacks unable to kill your characters for much of the fight.