I personally thought Hamilton was more intimidating...his quiet but massive self-confidence (the slight smirk on his face every time he spoke to Angel), his patience, etc. I know Caleb was powerful but his preacher boy persona & misogyny appeared to be because of old and deep personal weakness. (possibly, he learned to hate women so much because they probably made him feel insecure, inferior and not good enough when he was young, and probably also as an adult; possibly, he became a preacher because he failed to solve his own problems and essentially requires something else to solve his problems for him, or to at least make Caleb feel that he no longer had to deal with those problems, etc. as a way to abandon responsibility for himself). Caleb is a monster created essentially from weakness, issues that could not be overcome. No matter how strong or powerful a guy like that becomes, they are never really intimidating or scary to me. I can only see Caleb the bed wetting boy behind the facade. I respect (and I'd be much more reluctant to take on) Hamilton's cool confidence, patience and hidden arrogance.
Just as villains though, Caleb was interesting, more interesting than Hamilton, but Hamilton was more intimidating. I agree Hamilton was underused...but Caleb also was underused in some respects.