I think the only reason why that worked in Tactics was because Warriors couldn't use Magic Runes. Their MP also wasn't dependant on their Magic, but on their Skill.
It's just that some of these "Skill"-Runes are effective and some are just a waste. I'd like to balance this a bit more.
Maybe you could have as a minigame a Rune-Crafter, who you bring Rune Pieces and he can make new Runes for you.
But that sounds definitely too complicated.
Although Warriors can't use Magic Runes as effectively as Magicians, we could make the skill runes look like this:
Level 1 - physical damage to one enemy + rune special effects if any
Level 2 - physical damage to all enemies + rune special effects if any
Level 3 - high physical damage to one enemy + rune special effects if any
Level 4 - ultimate attack OR self-buffs + rune-specific penalty intended solely for balance.
For example, the Lion Rune (skill rune for Claw/Knuckle users) can have this skill set:
Level 1 - 1.5x damage to one enemy
Level 2 - 1.2x damage to all enemies
Level 3 - MAG - 25%, amount added to ATK, does not affect rune slots
Level 4 - consumes all MP to deal 3x damage to one enemy
Calculation for level 4 skill damage = (Attack - Defense) * (3 + Lv1 MP * 0.25 + Lv2 MP * 0.5 + Lv3 MP * 0.75 + Lv4 MP )