Badass Pacifist: He finally gets himself free from the chains that bound him whenever the other Jubei comes out and stops the attacks coming from Jubei and Nia. Then he bows down to Yoshihiko so that they can stop fighting already.
Blessed with Suck: Let's take a look at this from another perspective. He kisses one of the girls, and she gets powered up. Unfortunately, Muneakira gets to be chained with an invisible force to the point he can't even fight. Now, if an enemy is Genre Savvy, then they'd gun for Muneakira already with no guard or whatsoever. This doesn't seem to apply to Sen and Yukimura - only "Dark" Jubei provokes the vulnerable mode so far.
It's revealed towards the end that his ability as a general is still imperfect at the beginning of the series so his contracts are imperfect and carries major drawbacks, both in power output and the mentioned weakness. After Muneakira mastered the ability, he no longer suffers the weakness.
Depower: By the end of episode 1 in season 2, Muneakira's General power is almost gone due to magic seal inflicted to him. It wasn't even that powerful to begin with, but now he can't even lift a sword. Thankfully it doesn't stop him from being able to make more Master Samurai...
Double Standard: Abuse, Female on Male: He suffers from getting hit by the other girls quite a bit. Sometimes by accident, but largely due to jealousy when another girl makes a move on him, such as when Gisen first shows up, and tries to forcefully seduce him. Although he was completely innocent, as he's dragged away by both Sen and Yukimura, both girls hit him on the head a few times as they think about how he seems to be acting improperly around other girls.
Nice Guy: When he's not being mistaken for a pervert anyway.
Non-Action Guy: Although he seems to have a reputation for being a Bad Ass, he's not seen doing much fighting. However, it could be justified because he's also a General, who by definition leads the troops, rather than actively takes part in the fighting. Still, one would think he'd show off his combat abilities a little more often, particularly as the girls like to fight over him sometimes.
The Strategist: He usually performs this role for the girls in combat, giving them guidance on what to do in the fight.
Took a Level in Badass: Muneakira takes several throughout the series.◦ In the second to last episode, he frees himself from the chains that bind him whenever Badass!Jubei appears.
During the last episode, along with everyone else, but Muneakira's transformation from a flustered everydude to a determined commander is especially striking.
Berserk Button: She gets extremely angry at Musashi after the latter attacks Muneakira when he tried to stop the duel between the two girls. Although Jubei's attack didn't seem to do anything to Musashi, the latter gives the former the win after seeing her powers slowly reawakening.
In a more lighthearted sense, she doesn't like being called "fake" by Musashi.
Clingy Jealous Girl: She gets extremely angry when Jubei gets extremely close to Muneakira, and especially when the latter kisses him in front of her. She also gets upset at Yukimura trying to kiss him in episode four of the first season, and later when he awakens Kanetsugu as a Master Samurai in episode 3 of season 2.
Demoted to Extra: For much of season 2. When he does have a brief appearance around episode 5, it's actually Sen masquerading as him in an attempt to cheat during a contest. He finally starts having more screentime around episode 9, but its still largely brief scenes.
Demoted to Extra: While she played an important part in the first season, during season 2, she's seen very briefly in the beginning of episode 1. Then she doesn't show up again until around episode 9 and even then, doesn't play a very big role.
My Master, Right or Wrong: While she does try to fight against some of his commands, such as killing off the other master samurai girls, when Yoshihiko is threatened, she puts her life on the line for him.
The Worf Effect: While she proved to be rather formidable foe in the first season, in the first episode of season 2, she, along with other master samurai Yoshihiko produced to combat Amakusa, gets handily defeated by the Dark Samurai. She's also easily defeated by Amakusa later in the season.
Friendly Enemy: While she really wants to battle Jubei, she still pays visits to their Maid Cafe while its open, and later even goes looking for the street attacker after Jubei tells her that several characters suspect Inshun of being said attacker in episode 9 of season 2.