I actually think the family aspect helps with this.
All fathers try (or should, at least) to be larger-than-life for their children. You want your kids to believe that you are always in control, always have the answers. Fathers don't get to be regular people with problems and doubts, they (and the mothers) have to be the not-quite-human bastion their kids rely on to help the world make sense. So Jon being in the picture means that Clark has to be the one with wisdom, he has to be the one who sees the big picture, and he has to have an answer. He can't go running to Pa Kent for advice every time Jon asks a tough question (and couldn't even if Pa was alive). So Jon sort of helps reinforce those traits in Clark. It just happens to correlate with some of the classic pre-Crisis personality traits you and I are such a big fan of.