in my SoR game i gave ultima to minwu because he had the highest spirit. although scott had more intelligence than minwu had spirit and his flare was on a higher level than minwus ultima but ultima still did more damage. i think its mainly based on spirit.
It is based on weapon/spell levels. Since Minwu has more spells than Scott, he tends to do more Ultima damage. Spirit/Intelligence have nothing to do with it.