I'm not sure I agree Jim Bob is "nicer" or all that normal a person, his massive control issues alone make him seem just as batshit as Michelle at times. I do think that he is better at connecting with his children than Michelle is (which isn't all that difficult after all), or at least at connecting with his daughters. With the sons there appears to be some sort of weird competitive relationship going on, especially once the boys reach puberty. I haven't watched all episodes, but I don't recall that many scenes where Jim Bob interacts with his sons unless he is competing against them in some capacity. I could be wrong but he seems a lot more stand-offish with the boys than the girls. And with the girls he's clearly playing favourites, giving more affection and attention to those who fawn over him and never disagree with his headship.
For example, I remember a scene where Boob, Jill and Jana were in some tourist shop (in South America somewhere I think) looking for a gift for Mechelle and Boob reveals his grand plan of buying a native dress, looking mighty pleased with himself. Jana then very meekly suggests that maybe they should be getting Michelle something more practical that she could actually use, and wow are the short seconds after extremely telling. Boob looks fantastically pissy and turns away, basically shutting her out, Jana looks upset and resigned like she knows she made a mistake in questioning him, Jill on the other hand immediately steps in and smooths things over by diverting attention to herself; she also clearly knows Jana made a big faux pas. That short scene really stood out to me because it, along with other things Jim Bob says and does, implies to me that his love and affection towards his kids is very much conditional. He is closer to and more affectionate towards his children than Michelle is, but the relationships he has with them must always be on his terms and I think he sees and values his kids mainly in conjunction to himself, not as individuals in their own right.