M = (Level*Strength)/256 + (Level*Agility)/256 + 2
This feels like the most elegant fix.
Bells (only two of them, the Diamond Bell and Tinklebell) that follow a similair formula M = (Level*Magic)/128 + (Level*Agility)/128 + 2 are gimped by the fact they have crappy Battle Power and then only use 50% and 100% of that Battle Power, so Bells still come out as weak back-up weapons for a Job that's basically a vehicle for a single action ability.
Throw expands resources, and thus it's quite okay to deal the damage that it does. It does not deal unreasonable amounts of damage IMO; Shuriken, for instance, still don't deal as much damage as a Two-Handed Death Sickle Berserker while beating the MP-driven 1000 Needles. That seems about fair.
The Chicken Knife is the most difficult nut to crack. As it stands, the player is punished for his or her courageous no-run playthrough by what's generally considered the weaker of two weapons. The Brave Blade is compatible with Two-Handed and Goblin Punch, but doesn't deal the raw amount of damage the Chicken Knife produces. All other Knives in the game are basically back-up weapons. While most Jobs can equip them, they're usually inferior to other weapons unless they serve a specific secondary purpose (Thief Knife, Air Knife, Main Gauche come to mind). While a single exception is perfectly viable, the sheer force of the Chicken Knife is exactly that: an exception to the rule. It would seem more fitting to have the Brave Blade the superior weapon as a reward, so I feel the Chicken Knife should fall under the same M formula all other Knives do.
But that's sketchy, since Chicken Knife already has a perfectly decent formula... it just produces questionable output when the other Knives/Whips/Bows formulae are considered.