Well Knives generally have two weaknesses
Because they split their attacks into two they essentially double the defense of the opponent. So if the opponent reduces damage by 20 points, they reduce the entire volley by 40 points. They have an impossible time against high defense opponents... or at least they should.
The other is that if you aren't getting a back attack, it is a wasted attack. While quite a few enemies prevent you from going there.
To balance knives just emphasize the above. Create more of a need for maneuvering with rogues.
If I am not mistaken the defense system in the EE has been changed to absorb a percentual not an abolute value of the damage, so 2 hits with a 10 damage weapon would deal the same amount as a single attack with a 20 dmg weapon.
Also 2 hits not only increases the chance to inflict your opponent a with a negative status effect, but also can cause status "combos" (chill + chill = freeze).
With only 3 AP weapon range becomes more of a factor, because getting attacked with something like a spear means that your char with a regular range weapon has to use 1/3 instead of ~1/10 of their APs to be able to retaliate.
