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Intelligence without strength is a feminine trait in naruto, demonstrated by how lip service is constantly being payed to characters like Sakura, Ino, and Temari are smart but we rarely see them actually using this intellegence in ways that wins battles that center physical strength. Shikamaru is in a similar place to these female characters, because hes canonically quite weak outside of his genius. The text itself associates him with feminity, pairing him with female characters for both of his fights in the chunin exams for example, as well as him having to be rescued in situations where almost every other male character would have been able to win by fighting to the death. Shikamaru has to be rescued twice pre-timeskip, first by Asuma during orochimarus invasion and then (humiliatingly) by a girl, Temari, in the Sasuke retrieval arc.

He also has no drive to "be the best like no one ever was." Where almost every other male character in Naruto has an innate desire to get stronger that is shaped by their worldview (Naruto wants to be stronger to be hokage, Sasuke wants to get stronger for revenge, Lee wants to prove hard work can beat natural talent etc.) Shikamaru's doesnt want to be a great ninja at all, he just wants to be a normal guy, which in his society, includes working as a ninja. However, his lack of drive sets him apart from the rest of the male characters in the cast, with his goals aligning closer to the goals of the female characters. Shikamaru wants to have a normal job, a wife, a picket fence, and 2.5 kids, this goal does not involve him getting stronger, and is more similar to the goals of the women in the cast, since it doesn't really center on getting stronger as much as it does attempting to achieve the status quo.

The role of gender in Naruto is wild if you go looking for it. Everyone jokes about the female characters getting shafted, but it's facinating if you look at all the characters that play on the edge.

In the series, Feminity is associated with maternity, healing, looking pretty, and stability. Peace, too, if that is defined as not being at war.

In that way, its very interesting to consider that the ultimate villian of Naruto is not a warrior fighting for his ideals, pursuing revenge, or attempting to conquer the world. It's a powerful woman whose goal is to remove the abilities that cause the conflict in the first place. Who traps her victims in a perfect dream, rather than hurting them.

And Sasuke's place is also interesting, as a almost an ultimate masculine force. Over the course of the series several otherwise 'masculine' women act 'out of character' around him; think Temari taking time in her first appearance to note Sasuke's looks, while in active argument with team seven. Just like Shikamaru needing sexism to 'prove' his masculinity, being attracted to Sasuke is, time and again, used to 'prove' characters are really women.

And then there's the outliers. Orochimaru, gender-queer and portrayed by much of the series as true evil, constantly messing with gender. They even express desire for Sasuke, and what could be more femine than that? And what 'redemtion' is offered to them?

Becoming a mother. That is what moves him from a monstrous antagonist experimenting on children and twisting the natural order...to someone still doing all those things, but now 'acceptable' to the villages. Now she has a kid and stays in her house and wears feminine clothing and doesn't try to change the world in any way.

Compare that to Tsunade. A woman who rises to the highest position in the Leaf...as a single woman with no children and a focus on healing. Whose trauma is tied in with failing to protect the men in her life, making a doctor unable to stomach blood. Whose recommendation to prevent casualties is never instituted, and serves more to shackle her female students into a support role. Consider how female ninja almost all display some healing ability throughout the series, and none of their male counterparts do.

And then we reach Kabuto. The single major male healer in the series. Who very much follows in Shikamaru's mold, his sexism explicitly coming from suggesting that women attached to men are weaker , and whose trip to becoming main antagonist requires him 'stealing' power he doesn't 'deserve' and turning aside from healing and choosing instead to revive the dead.

For much of the series he remains a nebulous antagonist, healing characters for no immediate benifit to himself, resiting Orochimaru's control, and getting in Sasuke's way. Yet he opposes Konoha. And when he become truely evil, the first thing he does is...ask for Sasuke. Something at no point in the rest of the series does he have any interest in. It could be Orochimaru's obsession coming out, but it feels more pointed. Healers are devoted to Sasuke. Women are devoted to Sasuke. And he becomes the only person healed by Kabuto for the rest of the series. As a twisted person, he needs not only to upend death itself but also...forcably control Sasuke.

And in the end, he earns the same treatment as Orochimaru. Assigned to childcare. Feminized in appearance (genderless clothes, a return to long hair, scarred to forever have masquera) and role, he is no longer a 'danger' simply because he has been given everything 'women' want - a stable home, children to care for - and therefore his massive power is completely neutered. Within the narrative, both he and Orochimaru choose to stay obedient to the villages, and the villages in turn reward them with everything they want. Outside the narrative, it stinks of upholding the status quo, 'fixing' the antagonists with children, and forcing the queerest antagonists into defined gender roles. By becoming female, they give up the right to make changes in the system, and can only uphold the same system that shattered their minds and forced them to comit atrocities long before they made the choice on their own.