In the case of one parent; the father is usually the one who abandon the hero (and family) to save the world/better one self/fullfill a personal dream (insert own choice). While the father is gone, it is the mother who suffers through everything. Usually, by the time the series have began the mother have already died (the hero is brought up by a caring female relative). More things the hero can blame the father for.
So, the hero spend most of the series (if not all) hunting down dear old dad only to find out that the guy had a perfect legitimate reason for leaving, and damn he's pretty cool. The two bond, but before long father gets killed and son goes on a vengeance spree lamenting the fact that he never had the chance to get to know dad. Whatever happens, the son becomes much more powerful than the father.
The other way it could go is that mother-dear is the one who is absent in the hero's life (death, divorce, left with the other man, pick your fav soapie storyline). Our poor hero have to put up with an overbearing, arrogant prick of a father who is, well, usually cooler than the hero. Much dislike on the hero's part and much snickering from the father's part. Not exactly the best example of child rearing, but oh well. And like the former example, usually the father is trying to tain the son (no matter how obscure the method) to be better than the father (who already kicks arse, and really is still so much cooler at carrying off everything).
Anyways, why is it that there seem to be more parents issues in shounen manga than shoujo manga. I'm not saying it's true for every case, but it does seem to be a general theme. Shounen heroes (usually) come from really screwed up families while shoujo heroines (on the whole) come from well adjusted, and loving families. I just thought it was amusing that's all (and probably says quite a bit about the psychology of several cultures, but let's not get into that now).
And
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