Perhaps some government agency that wants to study the baby's super - genes could be antagonists. They would try to take the baby away from Lois and Clark, believing that they can use the baby's powers for the greater good of the country, but not realizing the harm it would cause to the family.
Lex Luthor could be a main antagonist. He might see the baby as a threat or a way to get to Clark. He could try to kidnap the baby to blackmail Clark into doing his bidding.
One possible plot could be the challenges they face as new parents while still dealing with their superhero and journalist duties. For example, Clark might have to rush off to save the world in the middle of a baby's feeding time, and Lois has to cover for him at home while also trying to meet a deadline for an important story.
One common theme is family bonding. Lois and Clark are often shown strengthening their relationship as they care for their baby together. Another theme is the balance between their normal lives and their superhero/journalist duties.
Love and sacrifice are also prevalent themes. They love their baby so much that they are willing to sacrifice a lot. Lois might sacrifice some big career opportunities to be with the baby, and Clark might risk his identity or even his life to keep the baby safe. These themes are what make Clark and Lois baby fanfiction so interesting and relatable.
Another possibility is that there is a mysterious figure who has some sort of vendetta against the family. This figure could be causing strange and unexplained events to occur around the baby, like making the baby sick in a way that doctors can't figure out at first. This would then be a source of conflict as Bella and Sam try to protect their baby from this unknown threat.
Maybe it could be a rival music producer who tries to use their new baby situation to create negative publicity for them. They might spread rumors about how having a baby will ruin their music careers.
Voldemort could be an antagonist if he somehow returns and sees the baby as a threat or a symbol of a new hope that he wants to destroy. He might target the baby to get back at Harry and Tom.
It could be their families if they are against the idea of Bella and Embry having a baby. For example, if Bella's family has high expectations for her and doesn't think Embry is a suitable partner, they could try to interfere and cause problems.
It could be a group of people who don't approve of Joel and Wednesday's relationship. They might try to separate the couple and take the baby away, believing that they are not fit parents because of their differences. Maybe some of Wednesday's more traditional family members who have a certain idea of how a family should be.
Maybe a rival guild that is jealous of Fairy Tail's new addition. They might think that having a baby with such strong magical potential in Fairy Tail gives them an unfair advantage. So they try to kidnap the baby to either keep it for themselves or use it to bargain with Fairy Tail.
Another great one is 'A Baby Changes Everything'. In this story, the baby becomes a symbol of hope for Metropolis. Lois and Clark are not only dealing with the joys and difficulties of raising a child but also how the baby affects their public image. It's a really interesting take on how their family life intersects with their roles in the city.