Why are a lot of characters in anime and manga named after their mothers and not their fathers? I've noticed this a lot in many manga I've read. The character (usually the protagonist) is named after their mother's family name and not their father's. Some examples I have found of this are as follows:


In Special A, Kei Takashima is named of his mother's family not his father's. Unless the parents were cousins, it seems the dad changed his name to Takashima, too.
In Naruto, Naruto Uzumaki is named after his mother Kushina Uzumaki. I know that this may be a plot device to hide who Naruto's father is at the beginning, but still why name after the mother? Why wasn't he named Namikaze?
In Shokugeki no Soma, Saiba Jouichiro changes his name to his wife's: Yukihira. Why doesn't he keep his name? It's possible that he wants to stay out of the public eye, but is it common for the man to take his wife's name?
Another example from the same manga as above, Azami Nakamura. He changed his name to Nakiri after marrying into Erina's mother's family. It could have been for prestige, but isn't it normally the wife who changes the name and not the husband? And Erina is named from her mother's family too.


Sorry for all the examples, but I really would like it if someone could help me understand. I know it could be because of a plot device, but it has confused me for a while.
Expanding my comment into an answer.

In Japan, it’s uncommon, but not unheard of, for a man to take his wife’s name after marriage. It can happen for any reason, but a common reason is when a man marries into a family with no sons and his wife’s family wants to keep their name going.

In modern Japan, married couples are required to pick one partner’s family name for both of them. From a Time article:


  In contrast, Japan requires that married couples take one of the spouses’ family names, which, unsurprisingly, means that 96% of married Japanese women assume their husband’s last name.


Any children of the marriage are given that last name as well, so if the couple chooses to use the wife’s name, the children will have their mother’s family name.

In anime, of course, this is used as a plot device, and the exact reason depends on the show. For instance, in Evangelion, Gendou takes Yui’s last name, Ikari, to try and distance himself from some of the unsavory things he did in the past. So Shinji gets his mother’s name, which might have various meanings, given all the Freudian subtext in the show.