A powerful and evil minion - like creature that has been banished for a long time could be the main villain. This creature sees the fem minions as traitors for teaming up with Luigi. It returns with a vengeance and tries to enslave all of them. It has the ability to control other minions and uses them to attack Luigi and the fem minions, creating a big battle scenario.
One idea could be that Luigi and the fem minions team up to save a magical kingdom. Luigi uses his skills like jumping and plumbing knowledge while the fem minions use their unique abilities and mischievousness to outwit the villains. Another could be a story where they all enter a cooking competition together, Luigi providing the human touch and the fem minions adding their own zany ingredients and cooking styles.
Mario would definitely be a main character. Since Luigi is his brother, he would be the one most concerned about Luigi's transformation and would do everything he could to help him. Princess Peach could also be a main character. She might offer her castle as a safe place for baby Luigi and use her resources to find a solution. Toad could be there too, helping Mario with taking care of Luigi and providing useful information about the kingdom that could lead to reversing the spell.
Another option could be a new character created specifically for this crossover. This character could be a wizard who has studied the ninja arts and has become corrupted by power. He could start by causing chaos in the wizarding world, using his magic to mimic some of the more dangerous ninja techniques. Then, he could set his sights on the ninja world, seeing it as another source of power to be conquered. Fem Naruto and Harry Potter would have to put aside their differences and work together to stop him.
Wario could also serve as an antagonist. He might be envious of Luigi's new married life and try to steal their treasures or disrupt their happiness. Maybe he spreads false rumors about Luigi in the Mushroom Kingdom just to create chaos in their lives.
Bowser could be the main antagonist. He might see Luigi's transformation as an opportunity to mess with Mario and the Mushroom Kingdom. He could try to use Luigi's new form to his advantage, perhaps by trying to make Luigi a spy or by using his new identity to cause chaos among the kingdom's residents.
Maybe a new character could be the main antagonist. A powerful and mysterious being that Luigi stumbles upon during his escape. This character might have some vendetta against the Mario brothers or just be generally evil and wants to stop Luigi's journey for its own malicious reasons.
Another option could be an evil version of Princess Peach. She could be possessed by some dark force. This would be a very interesting antagonist as Mario and Luigi would be hesitant to fight her at first because of their loyalty to the real Peach. But as she causes more and more chaos, they'd have to find a way to save her and the kingdom without harming her.
Peach could be an important character. As a friend of Daisy and a princess in the Mushroom Kingdom, she could offer her wisdom on raising a child. Also, Yoshi could be there. Yoshi is always friendly and could be like a protector for the baby, watching over it when Luigi and Daisy are busy.
Maybe some of the younger ninjas from the Leaf Village could be his minions. They look up to Naruto and would be eager to follow him.
Thanos could also be a good option. Imagine Bella's planet holds one of the Infinity Stones that Thanos needs. He would stop at nothing to get it, and Bella and the Avengers would have to join forces to protect it. Thanos' brute strength and strategic mind would pose a huge challenge for them.