How, I see it is that the stats for Power, Wisdom and Courage effect the game as following:
Power => determines Link's attack and defensive level.
Wisdom => determines Link's evasiveness and magical effect.
Courage => determines Link's speed and critical hit ratio.
What about different armor, swords, boots, etc. Dunno if somebody beat me to this yet. 
That could work as well. Perhaps there can be different settings to armour,swords and boots to favour one of the goddesses. Would that work?
Zora Tunic = Wisdom, since you are using a unique method of dealing with the common problem that is drowning.
Goron Tunic = Power, as it makes you strong enough to withstand great heat.
Kokiri Tunic = Courage. You have to be courageous to use something as useless as this.
Just leave the tunics as they are. As elemental resistance and weakness. The same goes for weapons like the fire and the ice arrow. Boots only allow you walk to certain places. Don't make things too complicated.
